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Malachowa N, Sturdevant DE, Porter AR, Martin G, Martens C, Nair V, Hansen B, Ricklefs S, Jenkins SG, Chen L, Kreiswirth BN, DeLeo FR. Insights into the molecular basis of reduced vancomycin susceptibility among three prominent Staphylococcus aureus clonal complexes. Microbiol Spectr 2024:e0048624. [PMID: 38916317 DOI: 10.1128/spectrum.00486-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/21/2024] [Indexed: 06/26/2024] Open
Abstract
Staphylococcus aureus is a leading cause of healthcare-associated infections globally. Vancomycin-resistant S. aureus (VRSA), those with high-level resistance [minimum inhibitory concentration (MIC) of 16-32 µg/mL vancomycin], are uncommon, whereas vancomycin-intermediate S. aureus (VISA; MIC of 4-8 µg/mL), are isolated more frequently and develop during long-term and/or repeated use of the antibiotic. VISA can be difficult to eradicate and infections may persist. Our knowledge of mechanisms that underlie the development of VISA is incomplete. We used a genomics approach to investigate the VISA phenotype in three prominent S. aureus lineages. All VISA clinical isolates tested had increased cell wall thickness compared with vancomycin-susceptible S. aureus strains. Growth rates of clonal complex (CC) 5, CC8, and CC45 clinical isolates were reduced in 2 µg/mL vancomycin compared to media alone. Culture in 2 and 4 µg/mL vancomycin sequentially for two weeks reduced susceptibility to daptomycin, televancin, tigecycline, and vancomycin in a majority of CC5, CC8, and CC45 isolates tested. We identified alleles reported previously to contribute to the VISA phenotype, but unexpectedly, these alleles were unique to each CC. A subtherapeutic concentration of vancomycin elicited changes in the VISA transcriptome-common and unique-among the three CCs tested. Multiple genes, including those encoding a glycerate kinase, an M50 family metallopeptidase, and an uncharacterized membrane protein, were upregulated among all three lineages and not reported previously as associated with VISA. Although there are lineage-specific changes in DNA sequence, our findings suggest changes in the VISA transcriptome constitute a general response to stress that confers reduced susceptibility to multiple antibiotics. IMPORTANCE Our understanding of the mechanisms that underlie the development of vancomycin-intermediate Staphylococcus aureus (VISA) is incomplete. To provide a more comprehensive view of this process, we compared genome sequences of clonal complex (CC) 5, CC8, and CC45 VISA clinical isolates and measured changes in the transcriptomes of these isolates during culture with a subtherapeutic concentration of vancomycin. Notably, we identified differentially expressed genes that were lineage-specific or common to the lineages tested, including genes that have not been previously reported to contribute to a VISA phenotype. Changes in gene expression were accompanied by reduced growth rate, increased cell wall thickness, and reduced susceptibility to daptomycin, televancin, tigecycline, and vancomycin. Our results provide support to the idea that changes in gene expression contribute to the development of VISA among three CCs that are a prominent cause of human infections.
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Affiliation(s)
- Natalia Malachowa
- Laboratory of Bacteriology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Daniel E Sturdevant
- Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Adeline R Porter
- Laboratory of Bacteriology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Grant Martin
- Laboratory of Bacteriology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Craig Martens
- Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Vinod Nair
- Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Bryan Hansen
- Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Stacy Ricklefs
- Research Technologies Branch, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Stephen G Jenkins
- Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Barry N Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Frank R DeLeo
- Laboratory of Bacteriology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
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Guo M, Jin Y, Wang H, Zhang X, Wu Y. Establishment of a Multilocus Sequence Typing Scheme for the Characterization of Avibacterium paragallinarum. Vet Sci 2024; 11:208. [PMID: 38787180 PMCID: PMC11125968 DOI: 10.3390/vetsci11050208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Infectious coryza is an acute respiratory infection caused by Avibacterium paragallinarum, which is widely distributed throughout the world. However, there is no effective molecular typing scheme to obtain basic knowledge about the Av. paragallinarum population structure. This study aimed to develop a multilocus sequence typing (MLST) scheme for Av. paragallinarum that allows for the worldwide comparison of sequence data. For this purpose, the genetic variability of 59 Av. paragallinarum strains from different geographical origins and serovars was analyzed to identify correlations. The MLST scheme was developed using seven conserved housekeeping genes, which identified eight STs that clustered all of the strains into three evolutionary branches. The analytical evaluation of the clone group relationship between the STs revealed two clone complexes (CC1 and CC2) and three singletons (ST2, ST5, and ST6). Most of the isolates from China belonged to ST1 and ST3 in CC1. ST8 from Peru and ST7 from North America together formed CC2. Our results showed that the Av. paragallinarum strains isolated from China had a distant genetic relationship with CC2, indicating strong regional specificity. The MLST scheme established in this study can monitor the dynamics and genetic differences of Av. paragallinarum transmission.
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Affiliation(s)
- Mengjiao Guo
- Jiangsu Co-Innovation Center for Prevention of Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.G.); (Y.J.); (H.W.); (X.Z.)
| | - Yikun Jin
- Jiangsu Co-Innovation Center for Prevention of Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.G.); (Y.J.); (H.W.); (X.Z.)
| | - Haonan Wang
- Jiangsu Co-Innovation Center for Prevention of Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.G.); (Y.J.); (H.W.); (X.Z.)
| | - Xiaorong Zhang
- Jiangsu Co-Innovation Center for Prevention of Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.G.); (Y.J.); (H.W.); (X.Z.)
| | - Yantao Wu
- Jiangsu Co-Innovation Center for Prevention of Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (M.G.); (Y.J.); (H.W.); (X.Z.)
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University (JIRLAAPS), Yangzhou 225009, China
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3
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Dominski BH, Raitz MDF, Provenzi MA, Silveira ACDO, Sincero TCM, Ferreira FA. Characterization of Methicillin-resistant Staphylococcus aureus (MRSA) isolated in Santa Catarina (SC), Brazil. Diagn Microbiol Infect Dis 2024; 109:116244. [PMID: 38452557 DOI: 10.1016/j.diagmicrobio.2024.116244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 02/05/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
The study investigated the characteristics of Methicillin-resistant Staphylococcus aureus (MRSA) isolated in Santa Catarina. Findings revealed prevalent SCCmecII and IV, multiresistance, Leucocidin ED genes, and one ST105 isolate. The results indicated that the in-state MRSA isolates showed the same characteristics as the out-of-state isolates among the investigated features.
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Affiliation(s)
- Bruno Hech Dominski
- Laboratório de Genética Molecular Bacteriana (GeMBac), Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina (UFSC), Campus Universitário Reitor João David Ferreira Lima, Trindade, Florianópolis, SC 88040-960, Brazil
| | - Maria de Fátima Raitz
- Laboratório de Genética Molecular Bacteriana (GeMBac), Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina (UFSC), Campus Universitário Reitor João David Ferreira Lima, Trindade, Florianópolis, SC 88040-960, Brazil
| | - Marcel Afonso Provenzi
- Laboratório de Genética Molecular Bacteriana (GeMBac), Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina (UFSC), Campus Universitário Reitor João David Ferreira Lima, Trindade, Florianópolis, SC 88040-960, Brazil
| | - Alessandro Conrado de Oliveira Silveira
- Departamento de Ciências Farmacêuticas, Fundação Universidade Regional de Blumenau (FURB). Rua Antônio da Veiga, 140. Itoupava Seca, Blumenau, SC 89030-903, Brazil
| | - Thais Cristine Marques Sincero
- Laboratório de Microbiologia Molecular Aplicada (MIMA); Departamento de Análises Clínicas, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina (UFSC), Campus Universitário Reitor João David Ferreira Lima, Trindade, Florianópolis, SC 88040-960, Brazil
| | - Fabienne Antunes Ferreira
- Laboratório de Genética Molecular Bacteriana (GeMBac), Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina (UFSC), Campus Universitário Reitor João David Ferreira Lima, Trindade, Florianópolis, SC 88040-960, Brazil.
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Boujemaa S, Suri GS, Kaur G. Multi-locus sequence typing of geographically and temporally diverse strains of Mycoplasma hominis. Diagn Microbiol Infect Dis 2024; 108:116207. [PMID: 38310740 DOI: 10.1016/j.diagmicrobio.2024.116207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/06/2024]
Abstract
This study aimed to investigate the genetic diversity of 108 geographically and temporally diverse strains of Mycoplasma hominis using a multi-locus sequence typing scheme (MLST). We extracted MLST data of 87 strains from PubMLST database and retrieved MLST gene sequences from 21 complete genomes of M. hominis available in GenBank database. MLST scheme identified 65 Sequence types (STs), which were grouped into five clonal complexes (CC) and 47 singletons. Phylogenetic analysis revealed that the majority of M. hominis isolates were clustered according to their country of origin, showing some significant specificity trends for the nation. Although recombination was detected, it was not significant enough to alter the clonal population structure of M. hominis. In sum, MLST scheme provides insightful data on the phylogenetics of international strains of M. hominis, arguing for the existence of genetically differentiable STs according to their origin of isolation.
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Affiliation(s)
- Safa Boujemaa
- Biologica Training and Consulting, Tunis, 2078, Tunisia.
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Yadav JP, Singh Y, Batra K, Khurana SK, Mahajan NK, Jindal N. Molecular detection of respiratory avian mycoplasmosis associated bacterial and viral concurrent infections in the poultry flocks. Anim Biotechnol 2023; 34:1474-1482. [PMID: 35112639 DOI: 10.1080/10495398.2022.2032725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Respiratory tract infections are of serious concern to the poultry industry. The present study was aimed to delineate the extent of respiratory avian mycoplasmosis associated bacterial and viral concurrent infections in the poultry flocks. A total of 146 poultry flocks of Haryana and Rajasthan, India, suspected for chronic respiratory disease (CRD) were screened for avian mycoplasmas, Newcastle disease virus (NDV), infectious bronchitis virus (IBV), and avian pathogenic Escherichia coli (APEC) by conventional polymerase chain reaction (PCR) assays. A total of 49.31% (72/146) flocks were found positive for Mycoplasma infection. Of the Mycoplasma-positive flocks, 80.55% (58/72) represented pathogenic avian mycoplasmas (MG and/or MS), while 19.44% (14/72) flocks were positive for commensal avian mycoplasmas (other than MG and MS). A correlation was deduced between avian mycoplasmosis and bacterial and/or viral co-infections. The results revealed that 17.24% (10/58) flocks had only avian mycoplasmosis infection. However, in the remaining flocks, the avian mycoplasmosis was associated either with APEC infection [17.24% (10/58)], IBV infection [43.10% (25/58)], or both APEC and IBV infections [22.41% (13/58)], respectively. Further epidemiological studies on respiratory avian mycoplasmosis associated concurrent infections with other pathogens are recommended to assess circulating strains, risk factors, and economic losses.
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Affiliation(s)
- Jay Prakash Yadav
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Yarvendra Singh
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Kanisht Batra
- Department of Animal Biotechnology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | | | - N K Mahajan
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Naresh Jindal
- Department of Veterinary Public Health and Epidemiology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
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Wu CF, Hsu CY, Chou CC, Wang CM, Huang SW, Kuo HC. Serotypes, virulence factors and multilocus sequence typing of Glaesserella parasuis from diseased pigs in Taiwan. PeerJ 2023; 11:e15823. [PMID: 37790626 PMCID: PMC10544350 DOI: 10.7717/peerj.15823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/10/2023] [Indexed: 10/05/2023] Open
Abstract
Background Glaesserella parasuis (G. parasuis) belongs to the normal microbiota of the upper respiratory tract in the swine, but virulent strains can cause systemic infections commonly known as Glässer's disease that leads to significant economic loss in the swine industry. Fifteen serotypes of G. parasuis have been classified by gel immunodiffusion test while the molecular serotyping based on variation within the capsule loci have further improved the serotype determination of unidentified field strains. Serovar has been commonly used as an indicator of virulence; however, virulence can be significantly differ in the field isolates with the same serotype. To date, investigations of G. parasuis isolated in Taiwan regarding antimicrobial resistance, serotypes, genotypes and virulence factors remain unclear. Methods A total of 276 G.parasuis field isolates were collected from 263 diseased pigs at the Animal Disease Diagnostic Center of National Chiayi University in Taiwan from January 2013 to July 2021. Putative virulence factors and serotypes of the isolates were identified by polymerase chain reaction (PCR) and antimicrobial susceptibility testing was performed by microbroth dilution assay. Additionally, the epidemiology of G. parasuis was characterized by multilocus sequence typing (MLST). Results Serotype 4 (33.3%) and 5 (21.4%) were the most prevalent, followed by nontypable isolates (15.9%), serotype 13 (9.4%), 12 (6.5%), 14 (6.2%), 7 (3.3%), 1 (1.8%), 9 (1.1%), 11 (0.7%) and 6 (0.4%). Nine out of 10 putative virulence factors showed high positive rates, including group 1 vtaA (100%), fhuA (80.4%), hhdA (98.6%), hhdB (96.0%), sclB7 (99.6%), sclB11 (94.9%), nhaC (98.2%), HAPS_0254 (85.9%), and cirA (99.3%). According to the results of antimicrobial susceptibility testing, ceftiofur and florfenicol were highly susceptible (>90%). Notably, 68.8% isolates showed multidrug resistance. MLST revealed 16 new alleles and 67 new sequence types (STs). STs of these isolated G. parasuis strains were classified into three clonal complexes and 45 singletons by Based Upon Related Sequence Types (BURST) analysis. All the G. parasuis strains in PubMLST database, including strains from the diseased pigs in the study, were defined into two main clusters by Unweighted Pair Group Method with Arithmetic Mean (UPGMA). Most isolates in this study and virulent isolates from the database were mainly located in cluster 2, while cluster 1 included a high percentage of nasal isolates from asymptomatic carriers. In conclusion, this study provides current prevalence and antimicrobial susceptibility of G. parasuis in Taiwan, which can be used in clinical diagnosis and treatment of Glässer's disease.
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Affiliation(s)
- Ching-Fen Wu
- Department of Veterinary Medicine, National Chiayi University, Chiayi City, Taiwan
| | - Chia-Yu Hsu
- Department of Veterinary Medicine, National Chiayi University, Chiayi City, Taiwan
| | - Chi-Chung Chou
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taichung, Taiwan
| | - Chao-Min Wang
- Department of Veterinary Medicine, National Chiayi University, Chiayi City, Taiwan
| | - Szu-Wei Huang
- Department of Veterinary Medicine, National Chiayi University, Chiayi City, Taiwan
| | - Hung-Chih Kuo
- Department of Veterinary Medicine, National Chiayi University, Chiayi City, Taiwan
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Kalpana S, Lin WY, Wang YC, Fu Y, Wang HY. Alternate Antimicrobial Therapies and Their Companion Tests. Diagnostics (Basel) 2023; 13:2490. [PMID: 37568853 PMCID: PMC10417861 DOI: 10.3390/diagnostics13152490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/14/2023] [Indexed: 08/13/2023] Open
Abstract
New antimicrobial approaches are essential to counter antimicrobial resistance. The drug development pipeline is exhausted with the emergence of resistance, resulting in unsuccessful trials. The lack of an effective drug developed from the conventional drug portfolio has mandated the introspection into the list of potentially effective unconventional alternate antimicrobial molecules. Alternate therapies with clinically explicable forms include monoclonal antibodies, antimicrobial peptides, aptamers, and phages. Clinical diagnostics optimize the drug delivery. In the era of diagnostic-based applications, it is logical to draw diagnostic-based treatment for infectious diseases. Selection criteria of alternate therapeutics in infectious diseases include detection, monitoring of response, and resistance mechanism identification. Integrating these diagnostic applications is disruptive to the traditional therapeutic development. The challenges and mitigation methods need to be noted. Applying the goals of clinical pharmacokinetics that include enhancing efficacy and decreasing toxicity of drug therapy, this review analyses the strong correlation of alternate antimicrobial therapeutics in infectious diseases. The relationship between drug concentration and the resulting effect defined by the pharmacodynamic parameters are also analyzed. This review analyzes the perspectives of aligning diagnostic initiatives with the use of alternate therapeutics, with a particular focus on companion diagnostic applications in infectious diseases.
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Affiliation(s)
- Sriram Kalpana
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan;
| | - Wan-Ying Lin
- Department of Medicine, University of California San Diego, San Diego, CA 92093, USA;
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA;
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Yu-Chiang Wang
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA;
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Yiwen Fu
- Department of Medicine, Kaiser Permanente Santa Clara Medical Center, Santa Clara, CA 95051, USA;
| | - Hsin-Yao Wang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan;
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA;
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
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Pustam A, Jayaraman J, Ramsubhag A. Comparative genomics and virulome analysis reveal unique features associated with clinical strains of Klebsiella pneumoniae and Klebsiella quasipneumoniae from Trinidad, West Indies. PLoS One 2023; 18:e0283583. [PMID: 37428714 DOI: 10.1371/journal.pone.0283583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/12/2023] [Indexed: 07/12/2023] Open
Abstract
Klebsiella pneumoniae and Klebsiella quasipneumoniae are closely related human pathogens of global concern. The more recently described K. quasipneumoniae shares similar morphological characteristics with K. pneumoniae and is commonly misidentified as this species using traditional laboratory techniques. The vast mobilome in these pathogenic bacteria influences the dissemination of virulence factors in high-risk environments and it is, therefore, critical to monitor strains for developing effective clinical management strategies. Herein, this study utilized Illumina sequencing to characterize the whole genomes of nine clinical K. pneumoniae and one K. quasipneumoniae isolate obtained from patients of 3 major hospitals in Trinidad, West Indies. Reconstruction of the assembled genomes and implementation of several bioinformatic tools revealed unique features such as high pathogenicity islands associated with the isolates. The K. pneumoniae isolates were categorized as classical (n = 3), uropathogenic (n = 5), or hypervirulent (n = 1) strains. In silico multilocus sequence typing, and phylogenetic analysis showed that isolates were related to several international high-risk genotypes, including sequence types ST11, ST15, ST86, and ST307. Analysis of the virulome and mobilome of these pathogens showed unique and clinically important features including the presence of genes associated with Type 1 and Type 3 fimbriae, the aerobactin and yersiniabactin siderophore systems, the K2 and O1/2, and the O3 and O5 serotypes. These genes were either on or in close proximity to insertion sequence elements, phage sequences, and plasmids. Several secretion systems including the Type VI system and relevant effector proteins were prevalent in the local isolates. This is the first comprehensive study investigating the genomes of clinical K. pneumoniae and K. quasipneumoniae isolates from Trinidad, West Indies. The data presented illustrate the diversity of Trinidadian clinical K. pneumoniae isolates as well as significant virulence biomarkers and mobile elements associated with these isolates. Additionally, the genomes of the local isolates will add to global databases and thus can be used in future surveillance or genomic studies in this country and the wider Caribbean region.
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Affiliation(s)
- Aarti Pustam
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
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Shashank PR, Parker BM, Rananaware SR, Plotkin D, Couch C, Yang LG, Nguyen LT, Prasannakumar NR, Braswell WE, Jain PK, Kawahara AY. CRISPR-based diagnostics detects invasive insect pests. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.541004. [PMID: 37292907 PMCID: PMC10245733 DOI: 10.1101/2023.05.16.541004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Rapid identification of organisms is essential across many biological and medical disciplines, from understanding basic ecosystem processes and how organisms respond to environmental change, to disease diagnosis and detection of invasive pests. CRISPR-based diagnostics offers a novel and rapid alternative to other identification methods and can revolutionize our ability to detect organisms with high accuracy. Here we describe a CRISPR-based diagnostic developed with the universal cytochrome-oxidase 1 gene (CO1). The CO1 gene is the most sequenced gene among Animalia, and therefore our approach can be adopted to detect nearly any animal. We tested the approach on three difficult-to-identify moth species (Keiferia lycopersicella, Phthorimaea absoluta, and Scrobipalpa atriplicella) that are major invasive pests globally. We designed an assay that combines recombinase polymerase amplification (RPA) with CRISPR for signal generation. Our approach has a much higher sensitivity than other real time-PCR assays and achieved 100% accuracy for identification of all three species, with a detection limit of up to 120 fM for P. absoluta and 400 fM for the other two species. Our approach does not require a lab setting, reduces the risk of cross-contamination, and can be completed in less than one hour. This work serves as a proof of concept that has the potential to revolutionize animal detection and monitoring.
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Affiliation(s)
- Pathour R. Shashank
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Division of Entomology, ICAR-Indian Agricultural Research Institution, New Delhi 110012, India
| | - Brandon M. Parker
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN 37831, USA
- U.S. Environmental Protection Agency, Office of Research and Development, RTP, NC, 27709, USA
| | - Santosh R. Rananaware
- Department of Chemical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - David Plotkin
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Christian Couch
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Lilia G. Yang
- Department of Chemical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Long T. Nguyen
- Department of Chemical Engineering, University of Florida, Gainesville, FL 32611, USA
| | - N. R. Prasannakumar
- Division of Crop Protection, ICAR-Indian Institute of Horticultural Research, Bengaluru 560089, India
| | - W. Evan Braswell
- Insect Management and Molecular Diagnostics Laboratory, USDA APHIS PPQ S&T, 22675 North Moorefield Road, Edinburg, Texas 78541, USA
| | - Piyush K. Jain
- Department of Chemical Engineering, University of Florida, Gainesville, FL 32611, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida, USA
| | - Akito Y. Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
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Kumawat M, Nabi B, Sharma P, Pal N, Sarma DK, Shubham S, Tiwari RR, Singh S, Kumar M. Assessment of multidrug-resistant profile, multi-locus sequence typing and efflux pump activity in Salmonella Typhimurium isolated from hospital sewage. World J Microbiol Biotechnol 2023; 39:162. [PMID: 37067651 DOI: 10.1007/s11274-023-03607-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/05/2023] [Indexed: 04/18/2023]
Abstract
Salmonella enterica serovar Typhimurium is becoming a leading cause of gastroenteritis and mortality. The use of antibiotics has increased natural resistance of S. Typhimurium to antibiotics. This study aims to isolate and characterize multi-drug-resistant (MDR) Salmonella strains from hospital sewage samples in Bhopal City, central India. The MDR isolates were characterized by molecular identification, antimicrobial resistance patterns, multi-locus sequence typing, and efflux pump activity. Specific genes (hilA, stn, invA, typh, and iroB) were used to confirm S. Typhimurium isolates. The Kirbey-Bauer method was employed to profile antimicrobial resistance using 20 antibiotics. Multi-locus sequence typing confirmed S. Typhimurium using seven housekeeping genes (aroC, dnaN, hemD, hisD, purE, sucA, and thr). Out of five strains, only four were confirmed as S. Typhimurium during MLST analysis. Efflux pump activity was determined using the ethidium bromide (EtBr) cartwheel test. Of the 160 isolates, 38 were presumptively confirmed as S. Typhimurium based on biochemical characterization, and only five MDR Salmonella strains were selected for their resistance against most antibiotics. Efflux pump activity revealed that five out of the four MDR isolates did not retain EtBr inside the cells, indicating pronounced efflux activity. Additionally, the isolated strains showed a specific correlation between the antimicrobial phenotypes and genotypes. The results of this study provide a better understanding of the characterization of S. Typhimurium serotype in Bhopal City. Future studies should focus on understanding changing antimicrobial resistance patterns, pathogenicity, and the genetic background of Salmonella serotypes. Further surveillance activities for antimicrobial-resistant Salmonella in different environmental sources should be prioritized.
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Affiliation(s)
- Manoj Kumawat
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, Madhya Pradesh, India
| | - Bilkees Nabi
- Department of Biochemistry & Biochemical Engineering, SHUATS, Allahabad, Uttar Pradesh, India
| | - Poonam Sharma
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, Madhya Pradesh, India
| | - Namrata Pal
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, Madhya Pradesh, India
| | - Devojit Kumar Sarma
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, Madhya Pradesh, India
| | - Swasti Shubham
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, Madhya Pradesh, India
| | - Rajnarayan R Tiwari
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, Madhya Pradesh, India
| | - Samradhi Singh
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, Madhya Pradesh, India
| | - Manoj Kumar
- Department of Microbiology, ICMR- National Institute for Research in Environmental Health, Bhopal, Madhya Pradesh, India.
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11
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Matsumoto Y, Nakamura S. Rapid and Comprehensive Identification of Nontuberculous Mycobacteria. Methods Mol Biol 2023; 2632:247-255. [PMID: 36781733 DOI: 10.1007/978-1-0716-2996-3_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Next-generation sequencing is a powerful tool to accurately identify pathogens. The MinION sequencer is best suited for the rapid identification of bacterial species due to its real-time sequence output. In this chapter, we introduce a method to identify nontuberculous mycobacteria (NTM) in one sequencing analysis from culture isolates using the MinION sequencer. NTM disease is now recognized as a growing global health concern due to its increasing incidence and prevalence. There are over 200 NTM species, of which the major pathogens are further classified into many subspecies showing different antibiotic susceptibilities. Therefore, identifying the pathogens at the subspecies level of NTM is necessary to select an appropriate treatment regimen. The protocol described here includes DNA extraction by lysis using silica beads, library preparation, sequencing by the MinION sequencer, and analysis of multilocus sequence typing using the software "mlstverse" and enables rapid and comprehensive identification of 175 species of NTM at the subspecies level with high sensitivity and accuracy.
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Affiliation(s)
- Yuki Matsumoto
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.
- Center for Infectious Disease Education and Research, Osaka University, Osaka, Japan.
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12
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Xing Y, Clark JR, Chang JD, Chirman DM, Green S, Zulk JJ, Jelinski J, Patras KA, Maresso AW. Broad protective vaccination against systemic Escherichia coli with autotransporter antigens. PLoS Pathog 2023; 19:e1011082. [PMID: 36800400 PMCID: PMC9937491 DOI: 10.1371/journal.ppat.1011082] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 12/26/2022] [Indexed: 02/18/2023] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) is the leading cause of adult life-threatening sepsis and urinary tract infections (UTI). The emergence and spread of multidrug-resistant (MDR) ExPEC strains result in a considerable amount of treatment failure and hospitalization costs, and contribute to the spread of drug resistance amongst the human microbiome. Thus, an effective vaccine against ExPEC would reduce morbidity and mortality and possibly decrease carriage in healthy or diseased populations. A comparative genomic analysis demonstrated a gene encoding an invasin-like protein, termed sinH, annotated as an autotransporter protein, shows high prevalence in various invasive ExPEC phylogroups, especially those associated with systemic bacteremia and UTI. Here, we evaluated the protective efficacy and immunogenicity of a recombinant SinH-based vaccine consisting of either domain-3 or domains-1,2, and 3 of the putative extracellular region of surface-localized SinH. Immunization of a murine host with SinH-based antigens elicited significant protection against various strains of the pandemic ExPEC sequence type 131 (ST131) as well as multiple sequence types in two distinct models of infection (colonization and bacteremia). SinH immunization also provided significant protection against ExPEC colonization in the bladder in an acute UTI model. Immunized cohorts produced significantly higher levels of vaccine-specific serum IgG and urinary IgG and IgA, findings consistent with mucosal protection. Collectively, these results demonstrate that autotransporter antigens such as SinH may constitute promising ExPEC phylogroup-specific and sequence-type effective vaccine targets that reduce E. coli colonization and virulence.
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Affiliation(s)
- Yikun Xing
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - Justin R. Clark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - James D. Chang
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - Dylan M. Chirman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sabrina Green
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jacob J. Zulk
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph Jelinski
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kathryn A. Patras
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anthony W. Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- TAILOR Labs, Vaccine Development Group, Baylor College of Medicine, Houston, Texas, United States of America
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13
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Hristova PM, Hitkova HY, Balgaranov NK, Gergova RТ, Alexandrova AS. Pediatric case of septic arthritis due to Streptococcus pneumoniae serotype 19A. Braz J Infect Dis 2023; 27:102742. [PMID: 36731539 PMCID: PMC9926192 DOI: 10.1016/j.bjid.2023.102742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/26/2022] [Accepted: 01/08/2023] [Indexed: 02/01/2023] Open
Abstract
In recent years, the incidence of pediatric septic arthritis caused by Streptococcus pneumoniae has been quite low. The pneumococcal conjugate vaccine PCV10 is the available vaccine included in the Bulgarian national immunization program. PCV10 reduces the incidence of invasive diseases, but non-vaccinal serotypes like 19A, the etiologic agent of the case of septic arthritis reported herein in a 3-year-old boy. The synovial fluid was positive for S. pneumoniae. The patient was treated with vancomycin during hospitalization and trimethoprim/sulfamethoxazole was recommended for at-home treatment. The isolate was subjected to latex agglutination, antimicrobial susceptibility testing, PCR detection for macrolide-resistance genes, and MLST. The strain revealed ST695 and a genotype previously associated with vaccine serotype 4. The incidence of pneumococcal infections caused by capsule-switching events and non-PCV10 serotypes is expected to increase.
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Affiliation(s)
- Preslava M Hristova
- Medical University - Pleven, Department of Microbiology and Virology, Pleven, Bulgaria.
| | - Hristina Y Hitkova
- Medical University - Pleven, Department of Microbiology and Virology, Pleven, Bulgaria
| | | | - Raina Т Gergova
- Medical University of Sofia, Department of Medical Microbiology, Sofia, Bulgaria
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14
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Shemirani MI, Tilevik D, Tilevik A, Jurcevic S, Arnellos D, Enroth H, Pernestig AK. Benchmarking of two bioinformatic workflows for the analysis of whole-genome sequenced Staphylococcus aureus collected from patients with suspected sepsis. BMC Infect Dis 2023; 23:39. [PMID: 36670352 PMCID: PMC9863170 DOI: 10.1186/s12879-022-07977-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 12/28/2022] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The rapidly growing area of sequencing technologies, and more specifically bacterial whole-genome sequencing, could offer applications in clinical microbiology, including species identification of bacteria, prediction of genetic antibiotic susceptibility and virulence genes simultaneously. To accomplish the aforementioned points, the commercial cloud-based platform, 1928 platform (1928 Diagnostics, Gothenburg, Sweden) was benchmarked against an in-house developed bioinformatic pipeline as well as to reference methods in the clinical laboratory. METHODS Whole-genome sequencing data retrieved from 264 Staphylococcus aureus isolates using the Illumina HiSeq X next-generation sequencing technology was used. The S. aureus isolates were collected during a prospective observational study of community-onset severe sepsis and septic shock in adults at Skaraborg Hospital, in the western region of Sweden. The collected isolates were characterized according to accredited laboratory methods i.e., species identification by MALDI-TOF MS analysis and phenotypic antibiotic susceptibility testing (AST) by following the EUCAST guidelines. Concordance between laboratory methods and bioinformatic tools, as well as concordance between the bioinformatic tools was assessed by calculating the percent of agreement. RESULTS There was an overall high agreement between predicted genotypic AST and phenotypic AST results, 98.0% (989/1006, 95% CI 97.3-99.0). Nevertheless, the 1928 platform delivered predicted genotypic AST results with lower very major error rates but somewhat higher major error rates compared to the in-house pipeline. There were differences in processing times i.e., minutes versus hours, where the 1928 platform delivered the results faster. Furthermore, the bioinformatic workflows showed overall 99.4% (1267/1275, 95% CI 98.7-99.7) agreement in genetic prediction of the virulence gene characteristics and overall 97.9% (231/236, 95% CI 95.0-99.2%) agreement in predicting the sequence types (ST) of the S. aureus isolates. CONCLUSIONS Altogether, the benchmarking disclosed that both bioinformatic workflows are able to deliver results with high accuracy aiding diagnostics of severe infections caused by S. aureus. It also illustrates the need of international agreement on quality control and metrics to facilitate standardization of analytical approaches for whole-genome sequencing based predictions.
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Affiliation(s)
- Mahnaz Irani Shemirani
- grid.8761.80000 0000 9919 9582Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Diana Tilevik
- grid.412798.10000 0001 2254 0954School of Bioscience, Systems Biology Research Centre, Infection Biology, University of Skövde, Skövde, Sweden
| | - Andreas Tilevik
- grid.412798.10000 0001 2254 0954School of Bioscience, Systems Biology Research Centre, Infection Biology, University of Skövde, Skövde, Sweden
| | - Sanja Jurcevic
- grid.412798.10000 0001 2254 0954School of Bioscience, Systems Biology Research Centre, Infection Biology, University of Skövde, Skövde, Sweden
| | | | - Helena Enroth
- grid.412798.10000 0001 2254 0954School of Bioscience, Systems Biology Research Centre, Infection Biology, University of Skövde, Skövde, Sweden ,Molecular Microbiology, Laboratory Medicine, Unilabs AB, Skövde, Sweden
| | - Anna-Karin Pernestig
- grid.412798.10000 0001 2254 0954School of Bioscience, Systems Biology Research Centre, Infection Biology, University of Skövde, Skövde, Sweden
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15
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Nykrynova M, Barton V, Bezdicek M, Lengerova M, Skutkova H. Identification of highly variable sequence fragments in unmapped reads for rapid bacterial genotyping. BMC Genomics 2022; 23:445. [PMID: 36581824 PMCID: PMC9798552 DOI: 10.1186/s12864-022-08550-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Bacterial genotyping is a crucial process in outbreak investigation and epidemiological studies. Several typing methods such as pulsed-field gel electrophoresis, multilocus sequence typing (MLST) and whole genome sequencing are currently used in routine clinical practice. However, these methods are costly, time-consuming and have high computational demands. An alternative to these methods is mini-MLST, a quick, cost-effective and robust method based on high-resolution melting analysis. Nevertheless, no standardized approach to identify markers suitable for mini-MLST exists. Here, we present a pipeline for variable fragment detection in unmapped reads based on a modified hybrid assembly approach using data from one sequencing platform. RESULTS In routine assembly against the reference sequence, high variable reads are not aligned and remain unmapped. If de novo assembly of them is performed, variable genomic regions can be located in created scaffolds. Based on the variability rates calculation, it is possible to find a highly variable region with the same discriminatory power as seven housekeeping gene fragments used in MLST. In the work presented here, we show the capability of identifying one variable fragment in de novo assembled scaffolds of 21 Escherichia coli genomes and three variable regions in scaffolds of 31 Klebsiella pneumoniae genomes. For each identified fragment, the melting temperatures are calculated based on the nearest neighbor method to verify the mini-MLST's discriminatory power. CONCLUSIONS A pipeline for a modified hybrid assembly approach consisting of reference-based mapping and de novo assembly of unmapped reads is presented. This approach can be employed for the identification of highly variable genomic fragments in unmapped reads. The identified variable regions can then be used in efficient laboratory methods for bacterial typing such as mini-MLST with high discriminatory power, fully replacing expensive methods such as MLST. The results can and will be delivered in a shorter time, which allows immediate and fast infection monitoring in clinical practice.
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Affiliation(s)
- Marketa Nykrynova
- grid.4994.00000 0001 0118 0988Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Vojtech Barton
- grid.4994.00000 0001 0118 0988Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Matej Bezdicek
- grid.412554.30000 0004 0609 2751Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czechia
| | - Martina Lengerova
- grid.412554.30000 0004 0609 2751Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czechia
| | - Helena Skutkova
- grid.4994.00000 0001 0118 0988Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
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16
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Sotthibandhu DS, Indoung S, Niwasawat H, Chaiboon J, Sungsorn N, Longji NI, Polya K, Noosak C, Schwarz S, Soimala T. The prevalence and antibiotic susceptibility of Staphylococcus spp. on ocular surfaces of fighting bulls ( Bos indicus) in Thailand. Vet World 2022; 15:2922-2928. [PMID: 36718321 PMCID: PMC9880847 DOI: 10.14202/vetworld.2022.2922-2928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/18/2022] [Indexed: 12/25/2022] Open
Abstract
Background and Aim fighting bulls have a high risk of eye injuries, and opportunistic conjunctival bacterial flora may cause subsequent eye diseases. There is little information about the ocular health care of fighting bulls in Thailand. Thus, this study aimed to estimate the prevalence of Staphylococcus spp. from the eyes of fighting bulls and investigate their antimicrobial susceptibility. Materials and Methods The samples were collected from the right conjunctival sacs of 105 fighting bulls. Biochemical tests and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry were used to identify bacteria to genus and species levels. Antimicrobial susceptibility was tested by agar disk diffusion. Results Staphylococcus spp. (36.84%, 56/152) were the most detected bacteria. The most prevalent Staphylococcus spp. was Staphylococcus chromogenes (37.50%, 21/56). The susceptibility test revealed that all isolates were susceptible to sulfamethoxazole/trimethoprim (56/56, 100%) and most were susceptible to chloramphenicol and gentamicin (54/56, 96.43%). The highest resistance rates were seen for tetracycline and doxycycline (23.21%, 13/56) followed by erythromycin (19.64%, 11/56). In addition, S. chromogenes isolates were evaluated for their ability to produce biofilms by a quantitative biofilm production assay. A total of 21 isolates exhibited biofilm production, independent of their antimicrobial susceptibility. Three multidrug-resistant isolates were found, including two Staphylococcus epidermidis isolates and a single S. chromogenes isolate. Conclusion As antimicrobial resistant bacteria were detected on the eye surface, veterinarians should always conduct antimicrobial susceptibility testing before using antimicrobial agents. The results from this study will help to improve the standard of eye treatment for fighting bulls in Thailand.
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Affiliation(s)
| | - Saowakon Indoung
- Faculty of Veterinary Science, Prince of Songkla University, Songkhla 90110, Thailand
| | - Husna Niwasawat
- Faculty of Veterinary Science, Prince of Songkla University, Songkhla 90110, Thailand
| | - Jiradchaya Chaiboon
- Faculty of Veterinary Science, Prince of Songkla University, Songkhla 90110, Thailand
| | - Nattakan Sungsorn
- Faculty of Veterinary Science, Prince of Songkla University, Songkhla 90110, Thailand
| | - Nu-issana Longji
- Faculty of Veterinary Science, Prince of Songkla University, Songkhla 90110, Thailand
| | - Kittipol Polya
- Thunderbolt fighting Bull Clinic, Songkhla 90110, Thailand
| | - Chayanee Noosak
- Faculty of Medical Technology, Prince of Songkla University, Songkhla 90110, Thailand
| | - Stefan Schwarz
- Department of Veterinary Medicine, Institute of Microbiology and Epizootics, Centre for Infection Medicine, Freie Universität Berlin, 14163 Berlin, Germany,Veterinary Centre for Resistance Research (TZR), Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
| | - Tanawan Soimala
- Faculty of Veterinary Science, Prince of Songkla University, Songkhla 90110, Thailand,Corresponding author: Tanawan Soimala, e-mail: Co-authors: DSS: , SI: , HN: , JC: , NS: , NL: , KP: , CN: , SS:
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17
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Osek J, Lachtara B, Wieczorek K. Listeria monocytogenes in foods-From culture identification to whole-genome characteristics. Food Sci Nutr 2022; 10:2825-2854. [PMID: 36171778 PMCID: PMC9469866 DOI: 10.1002/fsn3.2910] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/06/2022] [Accepted: 04/19/2022] [Indexed: 12/03/2022] Open
Abstract
Listeria monocytogenes is an important foodborne pathogen, which is able to persist in the food production environments. The presence of these bacteria in different niches makes them a potential threat for public health. In the present review, the current information on the classical and alternative methods used for isolation and identification of L. monocytogenes in food have been described. Although these techniques are usually simple, standardized, inexpensive, and are routinely used in many food testing laboratories, several alternative molecular-based approaches for the bacteria detection in food and food production environments have been developed. They are characterized by the high sample throughput, a short time of analysis, and cost-effectiveness. However, these methods are important for the routine testing toward the presence and number of L. monocytogenes, but are not suitable for characteristics and typing of the bacterial isolates, which are crucial in the study of listeriosis infections. For these purposes, novel approaches, with a high discriminatory power to genetically distinguish the strains during epidemiological studies, have been developed, e.g., whole-genome sequence-based techniques such as NGS which provide an opportunity to perform comparison between strains of the same species. In the present review, we have shown a short description of the principles of microbiological, alternative, and modern methods of detection of L. monocytogenes in foods and characterization of the isolates for epidemiological purposes. According to our knowledge, similar comprehensive papers on such subject have not been recently published, and we hope that the current review may be interesting for research communities.
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Affiliation(s)
- Jacek Osek
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
| | - Beata Lachtara
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
| | - Kinga Wieczorek
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
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18
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Fu M, He P, OuYang X, Yu Y, Wen B, Zhou D, Xiong X, Yuan Q, Jiao J. Novel genotypes of Coxiella burnetii circulating in rats in Yunnan Province, China. BMC Vet Res 2022; 18:204. [PMID: 35624449 PMCID: PMC9137106 DOI: 10.1186/s12917-022-03310-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Coxiella burnetii (Cb) is the causative agent of the zoonotic disease Q fever which is distributed worldwide. Molecular typing of Cb strains is essential to find out the infectious source and prevent Q fever outbreaks, but there has been a lack of typing data for Cb strains in China. The aim of this study was to investigate the genotypes of Cb strains in wild rats in Yunnan Province, China. RESULTS Eighty-six wild rats (Rattus flavipectus) were collected in Yunnan Province and 8 of the 86 liver samples from the wild rats were positive in Cb-specific quantitative PCR (qPCR). The Cb strains from the 8 rats were then typed into 3 genotypes using 10-spacer multispacer sequence typing (MST), and 2 of the 3 genotypes were recognized as novel ones. Moreover, the Cb strains in the wild rats were all identified as genotype 1 using 6-loci multilocus variable number of tandem repeat analysis (MLVA). CONCLUSIONS This is the first report of genotypic diversity of Cb strains from wild rats in China. Further studies are needed to explore the presence of more genotypes and to associate the genotypes circulating in the wildlife-livestock interaction with those causing human disease to further expand on the epidemiological aspects of the pathogen.
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Affiliation(s)
- Mengjiao Fu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Peisheng He
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.,Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, People's Republic of China
| | - Xuan OuYang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Yonghui Yu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Bohai Wen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Xiaolu Xiong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China
| | - Qinghong Yuan
- Yunnan Institute of Endemic Diseases Control and Prevention, Yunnan Provincial Key Laboratory of Natural Focal Disease Control and Prevention, Yunnan, People's Republic of China.
| | - Jun Jiao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People's Republic of China.
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Whole genome sequencing of Klebsiella pneumoniae clinical isolates sequence type 627 isolated from Egyptian patients. PLoS One 2022; 17:e0265884. [PMID: 35320327 PMCID: PMC8942217 DOI: 10.1371/journal.pone.0265884] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 03/09/2022] [Indexed: 12/13/2022] Open
Abstract
Klebsiella pneumoniae is considered a threat to public health especially due to multidrug resistance emergence. It is largely oligoclonal based on multi-locus sequence typing (MLST); in Egypt, ST 627 was recently detected. Despites the global dissemination of this ST, there is still paucity of information about it. Herein, we used 4 K. pneumoniae ST627 for whole genome sequencing utilizing an Illumina MiSeq platform. Genome sequences were examined for resistance and virulence determinants, capsular types, plasmids, insertion sequences, phage regions, and Clustered Regularly Interspaced Palindromic Repeats (CRISPR) regions using bioinformatic analysis. The molecular characterization revealed 15 and 65 antimicrobial resistance and virulence genes, respectively. Resistance genes such as tet(D), aph(3’’)-Ib, aph(6)-Id, blaTEM-234, fosA, and fosA6; were mainly responsible for tetracycline, aminoglycoside, and fosfomycin resistance; respectively. The capsular typing revealed that the four strains are KL-24 and O1v1. One plasmid was found in all samples known as pC17KP0052-1 and another plasmid with accession no. NZ_CP032191.1 was found only in K90. IncFIB(K) and IncFII(K) are two replicons found in all samples, while ColRNAI replicon was found only in K90. Entero P88, Salmon SEN5, and Klebsi phiKO2 intact phage regions were identified. All samples harbored CRISPR arrays including CRISPR1 and CRISPR2. Our results shed light on critical tasks of mobile genetic elements in ST 627 in antibiotic resistance spreading.
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Zhang S, Abbas M, Rehman MU, Wang M, Jia R, Chen S, Liu M, Zhu D, Zhao X, Gao Q, Tian B, Cheng A. Updates on the global dissemination of colistin-resistant Escherichia coli: An emerging threat to public health. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 799:149280. [PMID: 34364270 DOI: 10.1016/j.scitotenv.2021.149280] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/22/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Colistin drug resistance is an emerging public health threat worldwide. The adaptability, existence and spread of colistin drug resistance in multiple reservoirs and ecological environmental settings is significantly increasing the rate of occurrence of multidrug resistant (MDR) bacteria such as Escherichia coli (E. coli). Here, we summarized the reports regarding molecular and biological characterization of mobile colistin resistance gene (mcr)-positive E. coli (MCRPEC), originating from diverse reservoirs, including but not limited to humans, environment, waste water treatment plants, wild, pets, and food producing animals. The MCRPEC revealed the abundance of clinically important resistance genes, which are responsible for MDR profile. A number of plasmid replicon types such as IncI2, IncX4, IncP, IncX, and IncFII with a predominance of IncI2 were facilitating the spread of colistin resistance. This study concludes the distribution of multiple sequence types of E. coli carrying mcr gene variants, which are possible threat to "One Health" perspective. In addition, we have briefly explained the newly known mechanisms of colistin resistance i.e. plasmid-encoded resistance determinant as well as presented the chromosomally-encoded resistance mechanisms. The transposition of ISApl1 into the chromosome and existence of intact Tn6330 are important for transmission and stability for mcr gene. Further, genetic environment of co-localized mcr gene with carbapenem-resistance or extended-spectrum β-lactamases genes has also been elaborated, which is limiting human beings to choose last resort antibiotics. Finally, environmental health and safety control measures along with spread mechanisms of mcr genes are discussed to avoid further propagation and environmental hazards of colistin resistance.
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Affiliation(s)
- Shaqiu Zhang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Muhammad Abbas
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Livestock and Dairy Development Department Lahore, Punjab 54000, Pakistan
| | - Mujeeb Ur Rehman
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Disease Investigation Laboratory, Livestock & Dairy Development Department, Zhob 85200, Balochistan, Pakistan
| | - Mingshu Wang
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Renyong Jia
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Shun Chen
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Mafeng Liu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Dekang Zhu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Xinxin Zhao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Qun Gao
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Bin Tian
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Anchun Cheng
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China.
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21
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Ndahetuye JB, Leijon M, Båge R, Artursson K, Persson Y. Genetic Characterization of Staphylococcus aureus From Subclinical Mastitis Cases in Dairy Cows in Rwanda. Front Vet Sci 2021; 8:751229. [PMID: 34869725 PMCID: PMC8637448 DOI: 10.3389/fvets.2021.751229] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/11/2021] [Indexed: 12/04/2022] Open
Abstract
Whole-genome sequencing was carried out on 30 Staphylococcus (S.) aureus isolates from dairy cows with subclinical mastitis from all five provinces of Rwanda. Twenty-five of the isolates produced enough sequence to be analyzed using core genome multilocus sequence typing (cg-MLST). The isolates group into three main clusters. The largest cluster contain isolates of sequence type (ST) 152 (n = 6) and the closely related ST1633 (n = 2). These sequence types have previously mainly been encountered in humans. The isolates of the second-largest cluster belong to ST5477 (n = 5),so far exclusively isolated from cows in Rwanda. The third cluster consists of isolates of ST97 (n = 4), which is a well-known bovine-adapted sequence type. These three clusters were all widespread over the country. Isolates of the usually human-adapted sequence types 1 (n = 2) and 5 (n= 1) were found and a single isolate of ST2430, previously found among humans in Africa. Finally, four isolates of novel sequence types were found: ST7108 (n = 2), ST7109 (n = 1), and ST7110 (n = 1). The blaZ penicillin resistance gene was found in 84% of the isolates and was in all cases corroborated by phenotypic resistance determination. Five (20%) of the isolates carried a tetracycline resistance gene, tet(K) or tetM, and three of these five also displayed phenotypic resistance while two isolates carried a tetM-gene but were yet tetracycline susceptible. Seven (28%) isolates carried the dfrG gene conferring resistance to trimethoprim. Four of these isolates indeed were resistant to trimethoprim while three isolates were sensitive. The str gene conferring resistance to aminoglycosides was found in three isolates; however, none of these displayed resistance to gentamycin. Our data revealed a high diversity of the sequence types of S. aureus isolates from cows with subclinical mastitis in Rwanda. Two major clusters of ST97 and ST5477 are likely to be bovine adapted and cause mastitis while the third cluster of ST152 usually have been found in humans and may signify a recent transmission of these types from human to cows, for example from hand milking. The high prevalence of this sequence type among dairy cows may pose zoonotic threat. The sequence types were widely distributed without any geographic correlation. Penicillin resistance, the most common type of resistance with a prevalence over 80%, but also tetracycline and trimethoprim resistance were displayed by several isolates.
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Affiliation(s)
- Jean Baptiste Ndahetuye
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Veterinary Medicine, College of Agriculture, Animal Sciences and Veterinary Medicine, University of Rwanda, Kigali, Rwanda
| | | | - Renée Båge
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Karin Artursson
- National Veterinary Institute, Uppsala, Sweden.,Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ylva Persson
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden.,National Veterinary Institute, Uppsala, Sweden
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Phenotypic and genotypic characteristics of non-invasive S. pneumoniae isolates recovered from PCV10-vaccinated children in Bulgaria. Indian J Med Microbiol 2021; 40:61-67. [PMID: 34772534 DOI: 10.1016/j.ijmmb.2021.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 10/08/2021] [Accepted: 10/10/2021] [Indexed: 11/22/2022]
Abstract
PURPOSE The non-invasive pneumococcal disease (NIPD) is a common infection during childhood. We aimed to define the clonal spread of pediatric non-invasive isolates recovered during the PCV10-period in Bulgaria concerning the serotype and antimicrobial susceptibility. MATERIALS AND METHODS Serogrouping/serotyping were performed using latex agglutination and capsular swelling reaction. Serogroup 6 strains were subjected to serotype-specific PCR's. The antibiotic susceptibilities were assessed by broth microdilution. MLST was performed to define the clonal composition. RESULTS We analyzed 154 pediatrics non-invasive S. pneumoniae isolates. The PCV10-vaccinated children were 94.1%. We disclosed 88% non-vaccine serotypes (NVTs) and 12% PCV10 - serotypes. All common serotypes among PCV10-vaccinated children (n = 145) were non-vaccine types (NVTs): 19A (13.8%), 6C (11.7%), 3 (9.6%), 15A (8.3%) and 23A (5.5%). Antimicrobial non-susceptibility showed highest levels in erythromycin (50.0%), oral penicillin (49.4%), clindamycin (45.4%), trimethoprim-sulfamethoxazole (43.5%), tetracycline (42.2%), and ceftriaxone (14.3%). The multidrug-resistant strains (MDR) were 51.3%. MDR-serotypes were 6C (20.2%), 19A (17.7%), 15A (11.4%), 19F (10.1%), and 23A (8.9%). MLST presented 17 clonal complexes (CCs) with prevalence of CC320, CC386, CC505, CC8029 and CC2613 clustered 83% MDR isolates. CONCLUSIONS All emergent pediatric non-invasive serotypes in our geographic area during the studied PCV10-period were NVTs (19A, 6C, 3, 15A, and 23A). The fifth widespread CCs: CC320, CC386, CC505, CC8029 and CC2613 clustered 83% MDR isolates. Future surveillance of vaccine-induced changes in the clonality and the antimicrobial resistance of the pneumococcal population is needed.
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Sequence-based typing of clinical and environmental Legionella pneumophila isolates in Shenyang, China. ACTA ACUST UNITED AC 2021; 39:383-389. [PMID: 34620473 DOI: 10.1016/j.eimce.2020.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 06/04/2020] [Indexed: 11/23/2022]
Abstract
INTRODUCTION We performed SBT (sequence-based typing) on clinical and environmental Legionellapneumophila isolates in Shenyang (China). We analyzed and compared the results with those obtained by PFGE (pulsed field gel electrophoresis). METHODS Twenty-two L. pneumophila isolates were collected from two patients with L. pneumophila infection, two hospitals, and 13 office buildings. There were two clinical isolates, one strain isolated from domestic tap water, another from shower water and 18 strains from cooling tower water. All these isolates were analyzed by SBT and PFGE methods. RESULTS The 22 isolates were divided into 7 types by SBT. Five isolates belonged to novel sequence types (ST2345, ST2344, ST2406, ST2407, and ST2408) and one isolate belonged to ST328. The STs were not obtained for two of the isolates. The remaining 14 isolates belonged to ST1. PFGE typing divided the 22 isolates into 14 pulsotypes. The main pulsotype was SYC, which included seven isolates. CONCLUSION Both typing methods showed that predominant clonal lines exist in the Shenyang region, with high levels of genetic polymorphisms. Five novel STs were identified, indicating a unique genetic composition of L. pneumophila strains in this region, which are significantly different from those found in other environmental water systems in the world.
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Deidda F, Bozzi Cionci N, Cordovana M, Campedelli I, Fracchetti F, Di Gioia D, Ambretti S, Pane M. Bifidobacteria Strain Typing by Fourier Transform Infrared Spectroscopy. Front Microbiol 2021; 12:692975. [PMID: 34589064 PMCID: PMC8473902 DOI: 10.3389/fmicb.2021.692975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/09/2021] [Indexed: 11/13/2022] Open
Abstract
Fourier transform infrared (FTIR) spectroscopy, a technology traditionally used in chemistry to determine the molecular composition of a wide range of sample types, has gained growing interest in microbial typing. It is based on the different vibrational modes of the covalent bonds between atoms of a given sample, as bacterial cells, induced by the absorption of infrared radiation. This technique has been largely used for the study of pathogenic species, especially in the clinical field, and has been proposed also for the typing at different subspecies levels. The high throughput, speed, low cost, and simplicity make FTIR spectroscopy an attractive technique also for industrial applications, in particular, for probiotics. The aim of this study was to compare FTIR spectroscopy with established genotyping methods, pulsed-field gel electrophoresis (PFGE), whole-genome sequencing (WGS), and multilocus sequence typing (MLST), in order to highlight the FTIR spectroscopy potential discriminatory power at strain level. Our study focused on bifidobacteria, an important group of intestinal commensals generally recognized as probiotics. For their properties in promoting and maintaining health, bifidobacteria are largely marketed by the pharmaceutical, food, and dairy industries. Strains belonging to Bifidobacterium longum subsp. longum and Bifidobacterium animalis subsp. lactis were taken into consideration together with some additional type strains. For B. longum subsp. longum, it was possible to discriminate the strains with all the methods used. Although two isolates were shown to be strictly phylogenetically related, constituting a unique cluster, based on PFGE, WGS, and MLST, no clustering was observed with FTIR. For B. animalis subsp. lactis group, PFGE, WGS, and MLST were non-discriminatory, and only one strain was easily distinguished. On the other hand, FTIR discriminated all the isolates one by one, and no clustering was observed. According to these results, FTIR analysis is not only equivalent to PFGE, WGS, and MLST, but also for some strains, in particular, for B. animalis subsp. lactis group, more informative, being able to differentiate strains not discernible with the other two methods based on phenotypic variations likely deriving from certain genetic changes. Fourier transform infrared spectroscopy has highlighted the possibility of using the cell surface as a kind of barcode making tracing strains possible, representing an important aspect in probiotic applications. Furthermore, this work constitutes the first investigation on bifidobacterial strain typing using FTIR spectroscopy.
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Affiliation(s)
| | - Nicole Bozzi Cionci
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | | | | | | | - Diana Di Gioia
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | - Simone Ambretti
- Microbiology Unit-University Hospital of Bologna Policlinico Sant'Orsola-Malpighi, Bologna, Italy
| | - Marco Pane
- Probiotical Research S.r.L., Novara, Italy
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25
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Rumpf C, Lange J, Schwartbeck B, Kahl BC. Staphylococcus aureus and Cystic Fibrosis-A Close Relationship. What Can We Learn from Sequencing Studies? Pathogens 2021; 10:pathogens10091177. [PMID: 34578208 PMCID: PMC8466686 DOI: 10.3390/pathogens10091177] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 01/13/2023] Open
Abstract
Staphylococcus aureus is next to Pseudomonas aeruginosa the most isolated pathogen from the airways of cystic fibrosis (CF) patients, who are often infected by a dominant S. aureus clone for extended periods. To be able to persist, the pathogen has to adapt to the hostile niche of the airways to counteract host defence, antibiotic therapy and the competition with coinfecting pathogens. S. aureus is equipped with many virulence factors including adhesins, toxins that are localized on the chromosome, on plasmids or are phage-related. S. aureus is especially versatile and adaptation and evolution of the pathogen occurs by the acquisition of new genes by horizontal gene transfer (HGT), changes in nucleotides (single nucleotide variations, SNVs) that can cause a selective advantage for the bacteria and become fixed in subpopulations. Methicillin-resistant S. aureus are a special threat to CF patients due to the more severe lung disease occurring in infected patients. Today, with decreasing costs for sequencing, more and more studies using S. aureus isolates cultured from CF patients are being published, which use whole genome sequencing (WGS), multilocus sequence typing (MLST) or spa-sequence typing (spa-typing) to follow the population dynamics of S. aureus, elucidate the underlying mechanisms of phenotypic variants, newly acquired resistance or adaptation to the host response in this particular niche. In the first part of this review, an introduction to the genetic make-up and the pathogenesis of S. aureus with respect to CF is provided. The second part presents an overview of recent studies and their findings using genotypic methods such as single or multilocus sequencing and whole genome sequencing, which identify factors contributing to the adaptation of S. aureus and its evolution in the airways of individuals with CF.
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Tracking Fecal Bacterial Dispersion from Municipal Wastewater to Peri-Urban Farms during Monsoon Rains in Hue City, Vietnam. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18189580. [PMID: 34574504 PMCID: PMC8468961 DOI: 10.3390/ijerph18189580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/08/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022]
Abstract
Disease outbreaks attributed to monsoon flood-induced pathogen exposure are frequently reported, especially in developing cities with poor sanitation. Contamination levels have been monitored in past studies, yet the sources, routes, and extents of contamination are not always clear. We evaluated pollution from municipal wastewater (MWW) discharge and investigated fecal contamination by Escherichia coli (E. coli) in three agricultural fields on the outskirts of Hue City, Vietnam. After E. coli concentration was determined in irrigation water (IRW), MWW, soil, vegetables (VEG), and manure, its dispersion from MWW was tracked using multilocus sequence typing (MLST) and phylogenetic analyses during the wet and dry seasons. IRW was severely contaminated; 94% of the samples were positive with E. coli exceeding the stipulated standards, while VEG contamination was very low in both seasons. The confirmed total number of isolates was comparable between the seasons; however, results from MLST and phylogenetic clustering revealed more links between the sites and samples to MWW during the wet season. The wet season had four mixed clusters of E. coli isolates from multiple locations and samples linked to MWW, while only one mixed cluster also linking MWW to IRW was observed during the dry season. The most prevalent sequence type (ST) complex 10 and two others (40 and 155) have been associated with disease outbreaks, while other STs have links to major pathotypes. Irrigation canals are significant routes for E. coli dispersion through direct links to the urban drainage-infested river. This study clarified the genotype of E. coli in Hue city, and the numerous links between the samples and sites revealed MWW discharge as the source of E. coli contamination that was enhanced by flooding.
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27
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Rapid high-resolution melting genotyping scheme for Escherichia coli based on MLST derived single nucleotide polymorphisms. Sci Rep 2021; 11:16572. [PMID: 34400722 PMCID: PMC8368041 DOI: 10.1038/s41598-021-96148-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/27/2021] [Indexed: 11/08/2022] Open
Abstract
Routinely used typing methods including MLST, rep-PCR and whole genome sequencing (WGS) are time-consuming, costly, and often low throughput. Here, we describe a novel mini-MLST scheme for Eschericha coli as an alternative method for rapid genotyping. Using the proposed mini-MLST scheme, 10,946 existing STs were converted into 1,038 Melting Types (MelTs). To validate the new mini-MLST scheme, in silico analysis was performed on 73,704 strains retrieved from EnteroBase resulting in discriminatory power D = 0.9465 (CI 95% 0.9726-0.9736) for mini-MLST and D = 0.9731 (CI 95% 0.9726-0.9736) for MLST. Moreover, validation on clinical isolates was conducted with a significant concordance between MLST, rep-PCR and WGS. To conclude, the great portability, efficient processing, cost-effectiveness, and high throughput of mini-MLST represents immense benefits, even when accompanied with a slightly lower discriminatory power than other typing methods. This study proved mini-MLST is an ideal method to screen and subgroup large sets of isolates and/or quick strain typing during outbreaks. In addition, our results clearly showed its suitability for prospective surveillance monitoring of emergent and high-risk E. coli clones'.
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28
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Varghese R, Daniel JL, Neeravi A, Baskar P, Manoharan A, Sundaram B, Manchanda V, Saigal K, Yesudhasan BL, Veeraraghavan B. Multicentric Analysis of Erythromycin Resistance Determinants in Invasive Streptococcus pneumoniae; Associated Serotypes and Sequence Types in India. Curr Microbiol 2021; 78:3239-3245. [PMID: 34223923 DOI: 10.1007/s00284-021-02594-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 06/25/2021] [Indexed: 11/24/2022]
Abstract
Streptococcus pneumoniae is the major cause of childhood pneumonia and related deaths in India. Widespread use of erythromycin for the treatment of pneumonia has led to the emergence of erythromycin resistance. Despite this increase in erythromycin resistance, there are very little data on resistance determinants from India. Hence, we aimed to perform the molecular characterization of erythromycin-resistant invasive pneumococcal isolates in India. In this study, 250 erythromycin-resistant invasive isolates obtained from four Indian hospitals between 2014 and 2019 were included. The isolates were reconfirmed by standard CDC protocols, followed by detection of erm(B), mef(A/E) genes, and screening for mutations in 23S rRNA, ribosomal proteins L4 and L22. Among the 250 erythromycin-resistant isolates, 46% (n = 114) and 35% (n = 87) carried the mef(A/E) gene and erm(B) gene, respectively; both genes were present in 8% (n = 20) of the isolates and 12% (n = 29) of the studied strains did not bear any of them. The major mutations associated with erythromycin resistance in 23S rRNA, such as A2060C, A2061G, and C2613G, were absent. The predominant serotypes were 19F, 14, 23F, 6A, 6B, 19A, and 9V. The major clonal complexes were CC320, followed by CC230 and CC63. The predominant gene was mef(A/E), and most of the serotypes were PCV13 (54%). This study contributes to the baseline understanding of the erythromycin resistance determinants associated with the serotypes and sequence types (ST) of Indian invasive S. pneumoniae.
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Affiliation(s)
- Rosemol Varghese
- Department of Clinical Microbiology, Christian Medical College, Vellore, 632004, TN, India
| | - Jones Lionel Daniel
- Department of Clinical Microbiology, Christian Medical College, Vellore, 632004, TN, India
| | - Ayyanraj Neeravi
- Department of Clinical Microbiology, Christian Medical College, Vellore, 632004, TN, India
| | - Pavithra Baskar
- Department of Clinical Microbiology, Christian Medical College, Vellore, 632004, TN, India
| | - Anand Manoharan
- The CHILDS Trust Medical Research Foundation, Chennai, TN, India
| | | | - Vikas Manchanda
- Department of Microbiology, Maulana Azad Medical College, New Delhi, Delhi, India
| | - Karnika Saigal
- Department of Microbiology, Chacha Nehru Bal Chikitsalaya, New Delhi, Delhi, India
| | - Binesh Lal Yesudhasan
- Department of Clinical Microbiology, Christian Medical College, Vellore, 632004, TN, India
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore, 632004, TN, India.
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Hu Y, Zhou H, Lu J, Sun Q, Liu C, Zeng Y, Zhang R. Evaluation of the IR Biotyper for Klebsiella pneumoniae typing and its potentials in hospital hygiene management. Microb Biotechnol 2021; 14:1343-1352. [PMID: 33205912 PMCID: PMC8313285 DOI: 10.1111/1751-7915.13709] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 10/29/2020] [Indexed: 02/02/2023] Open
Abstract
Klebsiella pneumoniae has emerged as one of the most important pathogens that frequently encounter in community-acquired or hospital-acquired infections. Timely epidemiological surveillance could greatly facilitate infection control of K. pneumoniae and many deadly pathogens alike. In this study, we evaluated the performance of the IR Biotyper, a Fourier transform infrared (FTIR) spectroscopy system for K. pneumoniae isolates typing through (i) optimizing the culture scheme and defining the cutoff value (COV) range and (ii) comparing with commonly used typing tools such as multi-locus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS). We found that a non-selective and non-chromogenic medium with 24 ± 2 h incubation gives the best discriminatory power for the IR Biotyper (IRBT). COV evaluation indicated that the IRBT is a robust typing method with good reproducibility. Besides, we observed that the modified H2 O-EtOH suspensions preparation method could enhance the quality of the spectrum, especially for those hypermucoviscous strains. For the method comparison study, our data demonstrated that FTIR spectroscopy could accurately cluster K. pneumoniae strains. The typing results of the IRBT were almost entirely in concordance with those from PFGE and WGS. Together with the advantages such as low costs and short turnaround time (less than 3h), the IRBT is a promising tool for strain typing that could make real-time outbreak investigation a reality.
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Affiliation(s)
- Yanyan Hu
- Clinical Microbiology LaboratorySchool of Medicine2nd Affiliated Hospital of Zhejiang UniversityZhejiang UniversityHangzhouChina
| | - Hongwei Zhou
- Clinical Microbiology LaboratorySchool of Medicine2nd Affiliated Hospital of Zhejiang UniversityZhejiang UniversityHangzhouChina
| | - Jiayue Lu
- Clinical Microbiology LaboratorySchool of Medicine2nd Affiliated Hospital of Zhejiang UniversityZhejiang UniversityHangzhouChina
| | - Qiaoling Sun
- Clinical Microbiology LaboratorySchool of Medicine2nd Affiliated Hospital of Zhejiang UniversityZhejiang UniversityHangzhouChina
| | - Congcong Liu
- Clinical Microbiology LaboratorySchool of Medicine2nd Affiliated Hospital of Zhejiang UniversityZhejiang UniversityHangzhouChina
| | - Yu Zeng
- Clinical Microbiology LaboratorySchool of Medicine2nd Affiliated Hospital of Zhejiang UniversityZhejiang UniversityHangzhouChina
| | - Rong Zhang
- Clinical Microbiology LaboratorySchool of Medicine2nd Affiliated Hospital of Zhejiang UniversityZhejiang UniversityHangzhouChina
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Hugenholtz P, Chuvochina M, Oren A, Parks DH, Soo RM. Prokaryotic taxonomy and nomenclature in the age of big sequence data. THE ISME JOURNAL 2021; 15:1879-1892. [PMID: 33824426 PMCID: PMC8245423 DOI: 10.1038/s41396-021-00941-x] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 02/01/2023]
Abstract
The classification of life forms into a hierarchical system (taxonomy) and the application of names to this hierarchy (nomenclature) is at a turning point in microbiology. The unprecedented availability of genome sequences means that a taxonomy can be built upon a comprehensive evolutionary framework, a longstanding goal of taxonomists. However, there is resistance to adopting a single framework to preserve taxonomic freedom, and ever increasing numbers of genomes derived from uncultured prokaryotes threaten to overwhelm current nomenclatural practices, which are based on characterised isolates. The challenge ahead then is to reach a consensus on the taxonomic framework and to adapt and scale the existing nomenclatural code, or create a new code, to systematically incorporate uncultured taxa into the chosen framework.
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Affiliation(s)
- Philip Hugenholtz
- grid.1003.20000 0000 9320 7537Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD Australia
| | - Maria Chuvochina
- grid.1003.20000 0000 9320 7537Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD Australia
| | - Aharon Oren
- grid.9619.70000 0004 1937 0538Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Edmond J. Safra campus, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Donovan H. Parks
- grid.1003.20000 0000 9320 7537Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD Australia
| | - Rochelle M. Soo
- grid.1003.20000 0000 9320 7537Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD Australia
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Alexandrova AS, Pencheva DR, Mitov IG, Setchanova LP. Clonal distribution, antimicrobial resistance, and pilus islets in S.pneumoniae isolates recovered from PCV10-vaccinated children with suppurative AOM in Bulgaria (2015-2020), BULGARIA. Jpn J Infect Dis 2021; 75:92-95. [PMID: 34193663 DOI: 10.7883/yoken.jjid.2021.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Streptococcus pneumoniae is still a leading bacterial pathogen of acute otitis media (AOM), despite the available pneumococcal conjugate vaccines (PCVs). We conducted a study on the population structure, antibiotic nonsusceptibility, serotype distribution, and presence of pilus in middle ear fluids - S. pneumoniae isolates recovered from PCV10-vaccinated children with suppurative АОМ in Bulgaria. Non-susceptibility was revealed in 68.75% (n=33) of the isolates. Multidrug-resistance (MDR) has been detected in 60.4%. The dual macrolide resistance mechanism was predominant. Most widespread were non-PCV10 serotypes 3 (27.1%, n=13), 19A (25.0%, n=12), and VT 19F (23.0%, n=11). A total of 64.6% were non-PCV10-serotypes. Presence of Pilus type I was observed mostly in PCV10-serotypes. We disclosed a strong association between CCs, serotype, and antimicrobial resistance. The MLST revealed the presence of four CCs: CC320 (39.6%), CC505 (12.5%), CC1377 8.3%), and CC230 (8.3%), respectively. The most abundant CC320 comprised MDR 19A and 19F isolates. CC230 clustered MDR isolates from serotype 19A, 6C, and 14. CC505 and CC1377 covered serotype 3 susceptible isolates. The vaccine-induced changes and trends in antimicrobial resistance and clonality must be an object of systematic investigations.
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Affiliation(s)
| | - Daniela Rosenova Pencheva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, Bulgaria
| | - Ivan Gergov Mitov
- Department of Medical Microbiology, Medical Faculty, Medical University of Sofia, Bulgaria
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Monitoring microbial growth on a microfluidic lab-on-chip with electrochemical impedance spectroscopic technique. Biomed Microdevices 2021; 23:26. [PMID: 33885989 DOI: 10.1007/s10544-021-00564-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2021] [Indexed: 12/17/2022]
Abstract
A continuous rise in the wastes from industrial effluents, bio-waste, and pharmaceuticals has deteriorated surface water and drinking water sources. Standard laboratory tests of total coliform are time-consuming and logistically inefficient for field data generation. Better and portable sensing technologies are needed. This paper reports an electrical impedance spectroscopic technique incorporated in a micro-fluidic chip with interdigitated microelectrodes to monitor the growth of microbial cells. Lag, log, and stationary phases of Escherichia coli cell growth with an integrated electrode are successfully detected, for samples of reverse osmosis water, standard treated tap water, and recycled water respectively. The results indicate that reverse osmosis water has a higher probability of contamination with bacterial pathogens compared to the other two types of water samples when subjected to the same amount of added nutrients. The statistical analysis shows a possible single detection range with higher-order regression, and repeat use of a single chip with the electrode was found to be within an acceptable limit. The interdigitated electrodes exposed to in-situ cell growth conditions and repeated electrical measurements have shown a promise for possible periodic or continuous monitoring. The paper further identifies several complimentary analysis methodologies that are robust towards phase noise in the measured impedance and are suited particularly for early-stage detection of bacterial contamination. The cell adhesion tendencies over the microelectrode due to the electric field need to be further analyzed.
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Eibl C, Baumgartner M, Urbantke V, Sigmund M, Lichtmannsperger K, Wittek T, Spergser J. An Outbreak of Subclinical Mastitis in a Dairy Herd Caused by a Novel Streptococcus canis Sequence Type (ST55). Animals (Basel) 2021; 11:ani11020550. [PMID: 33672442 PMCID: PMC7923261 DOI: 10.3390/ani11020550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/13/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Although Streptococcus (S). canis is mainly isolated from carnivores, intramammary infection in dairy cows caused by this bacterium have been reported. Cats and dogs with access to the barn have been considered as the main source of these infections. Here, we report subclinical mastitis and substantially increased bulk milk somatic cell counts in a dairy herd. During a herd visit, management and hygiene practices were evaluated and data from the milk quality control program were retrieved. Furthermore, quarter milk samples, mucosal swabs from farm cats and a dog, and swabs from the milking unit were aseptically collected. The samples were examined bacteriologically, and S. canis was identified using conventional phenotypic methods and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Genetic relationships between S. canis isolates were determined by multilocus sequence typing, revealing that all S. canis isolates shared the same sequence type, presenting a new combination of alleles for which a new number (ST55) was assigned. As the most likely source of intramammary infection, a farmyard cat was identified. The concurrent treatment of all positive cows and the improvement of management (no further access of carnivores to the barn) lead to positive results, including a decreased somatic cell count. Abstract The present case report provides data on the phenotypic and genotypic properties of S. canis isolated from nine dairy cows with subclinical mastitis (SCC greater than 200,000 cells/mL in the quarter milk sample, no clinical signs) and from a cat living in the barn and reports the eradication of the pathogen from the herd with an automatic milking system. The isolates were identified using conventional bacteriology, matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) and genetic relationships were investigated by multilocus sequence typing (MLST). Udder health management and hygiene instructions comprised the removal of the carnivores from the barn, strict monitoring of milking hygiene and techniques to avoid new infections via the milking robot, with simultaneous therapy for all infected cows. Phenotypic and genotypic properties of all isolates were identical. MLST revealed a unique sequence type (ST55) and a farmyard cat was identified as the most likely source of the S. canis infection in cows. The simultaneous treatment of all infected cows and management and hygiene improvements lead to a decreased SCC within four weeks.
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Affiliation(s)
- Cassandra Eibl
- University Clinic for Ruminants, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria; (M.B.); (V.U.); (M.S.); (K.L.); (T.W.)
- Correspondence: ; Tel.: +43-1-25077-5203
| | - Martina Baumgartner
- University Clinic for Ruminants, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria; (M.B.); (V.U.); (M.S.); (K.L.); (T.W.)
| | - Verena Urbantke
- University Clinic for Ruminants, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria; (M.B.); (V.U.); (M.S.); (K.L.); (T.W.)
| | - Michael Sigmund
- University Clinic for Ruminants, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria; (M.B.); (V.U.); (M.S.); (K.L.); (T.W.)
| | - Katharina Lichtmannsperger
- University Clinic for Ruminants, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria; (M.B.); (V.U.); (M.S.); (K.L.); (T.W.)
| | - Thomas Wittek
- University Clinic for Ruminants, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria; (M.B.); (V.U.); (M.S.); (K.L.); (T.W.)
| | - Joachim Spergser
- Institute of Microbiology, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria;
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Baker KS. Microbe hunting in the modern era: reflecting on a decade of microbial genomic epidemiology. Curr Biol 2020; 30:R1124-R1130. [PMID: 33022254 PMCID: PMC7534602 DOI: 10.1016/j.cub.2020.06.097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Since the first recognition that infectious microbes serve as the causes of many human diseases, physicians and scientists have sought to understand and control their spread. For the past 150+ years, these ‘microbe hunters’ have learned to combine epidemiological information with knowledge of the infectious agent(s). In this essay, I reflect on the evolution of microbe hunting, beginning with the history of pre-germ theory epidemiological studies, through the microbiological and molecular eras. Now in the genomic age, modern-day microbe hunters are combining pathogen whole-genome sequencing with epidemiological data to enhance epidemiological investigations, advance our understanding of the natural history of pathogens and drivers of disease, and ultimately reshape our plans and priorities for global disease control and eradication. Indeed, as we have seen during the ongoing Covid-19 pandemic, the role of microbe hunters is now more important than ever. Despite the advances already made by microbial genomic epidemiology, the field is still maturing, with many more exciting developments on the horizon.
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Affiliation(s)
- Kate S Baker
- University of Liverpool, Institute for Infection, Ecology and Veterinary Sciences, Department of Clinical Infection, Microbiology, and Immunology, Liverpool L69 7ZB, UK.
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Zakaria Z, Hassan L, Sharif Z, Ahmad N, Ali RM, Husin SA, Hazis NHBA, Sohaimi NFM, Bakar SA, Garba B. Analysis of Salmonella enterica serovar Enteritidis isolates from chickens and chicken meat products in Malaysia using PFGE, and MLST. BMC Vet Res 2020; 16:393. [PMID: 33069231 PMCID: PMC7568380 DOI: 10.1186/s12917-020-02605-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 10/01/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Salmonella is a very important foodborne pathogen causing illness in humans. The emergence of drug-resistant strains also constitutes a serious worry to global health and livestock productivity. This study investigated Salmonella isolates from chicken and chicken meat products using the phenotypic antimicrobial screening as well as the molecular characteristics of Salmonella isolates. Upon serotyping of the isolates, the antimicrobial susceptibility profiling using a panel of 9 commonly used antimicrobials was done. Subsequently, the molecular profiles of all the isolates were further determined using Pulsed Field Gel Electrophoresis (PFGE) and the Whole Genome Multi-Locus Sequence Type (wgMLST) analysis in order to obtain the sequence types. RESULTS The PFGE data was input into FPQuest software, and the dendrogram generated was studied for possible genetic relatedness among the isolates. All the isolates were found to belong to the Salmonella Enteritidis serotype with notable resistance to tetracycline, gentamycin, streptomycin, and sulfadimidine. The S. Enteritidis isolates tested predominantly subtyped into the ST11 and ST1925, which was found to be a single cell variant of ST11. The STs were found to occur in chicken meats, foods, and live chicken cloacal swabs, which may indicate the persistence of the bacteria in multiple foci. CONCLUSION The data demonstrate the presence of S. Enteritidis among chickens, indicating its preference and reservoir status for enteric Salmonella pathogens.
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Affiliation(s)
- Zunita Zakaria
- Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
- Bacteriology Laboratory, Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Latiffah Hassan
- Bacteriology Laboratory, Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Department of Veterinary Laboratory Diagnostics, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Zawiyah Sharif
- Food Safety and Quality Division, Ministry of Health, 62675, Putrajaya, Malaysia
| | - Norazah Ahmad
- Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Setia Alam, Selangor, Malaysia
| | - Rohaya Mohd Ali
- Diagnostic and Quality Assurance Division, Department of Veterinary Services, Ministry of Agriculture & Agro-Based Industry, Putrajaya, Malaysia
| | - Suraya Amir Husin
- Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Setia Alam, Selangor, Malaysia
| | - Nor Hazrin Binti Abd Hazis
- Infectious Diseases Research Centre, Institute for Medical Research, National Institutes of Health, Setia Alam, Selangor, Malaysia
| | - Nor Fitriah Mohamed Sohaimi
- Bacteriology Laboratory, Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Shafini Abu Bakar
- Food Safety and Quality Division, Ministry of Health, 62675, Putrajaya, Malaysia
| | - Bashiru Garba
- Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Faculty of Veterinary Medicine, Usmanu Danfodiyo University, Sultan Abubakar Road, City Campus Complex, Sokoto, Sokoto State, 840212, Nigeria
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Population diversity and virulence characteristics of Cryptococcus neoformans/C. gattii species complexes isolated during the pre-HIV-pandemic era. PLoS Negl Trop Dis 2020; 14:e0008651. [PMID: 33017391 PMCID: PMC7535028 DOI: 10.1371/journal.pntd.0008651] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 07/27/2020] [Indexed: 11/19/2022] Open
Abstract
Cryptococcosis has become a major global health problem since the advent of the HIV pandemic in 1980s. Although its molecular epidemiology is well-defined, using isolates recovered since then, no pre-HIV-pandemic era epidemiological data exist. We conducted a molecular epidemiological study using 228 isolates of the C. neoformans/C. gattii species complexes isolated before 1975. Genotypes were determined by URA5 restriction fragment length polymorphism analysis and multi-locus sequence typing. Population genetics were defined by nucleotide diversity measurements, neutrality tests, and recombination analysis. Growth at 37°C, melanin synthesis, capsule production, and urease activity as virulence factors were quantified. The pre-HIV-pandemic isolates consisted of 186 (81.5%) clinical, 35 (15.4%) environmental, and 7 (3.1%) veterinary isolates. Of those, 204 (89.5%) belonged to C. neoformans VNI (64.0%), VNII (14.9%) and VNIV (10.5%) while 24 (10.5%) belonged to C. gattii VGIII (7.5%), VGI (2.6%) and VGII (0.5%). Among the 47 sequence types (STs) identified, one of VNII and 8 of VNIV were novel. ST5/VNI (23.0%) in C. neoformans and ST75/VGIII (25.0%) in C. gattii were the most common STs in both species complexes. Among C. neoformans, VNIV had the highest genetic diversity (Hd = 0.926) and the minimum recombination events (Rm = 10), and clinical isolates had less genetic diversity (Hd = 0.866) than environmental (Hd = 0.889) and veterinary isolates (Hd = 0.900). Among C. gattii, VGI had a higher nucleotide diversity (π = 0.01436) than in VGIII (π = 0.00328). The high-virulence genotypes (ST5/VNI and VGIIIa/serotype B) did not produce higher virulence factors levels than other genotypes. Overall, high genetic variability and recombination rates were found for the pre-HIV-pandemic era among strains of the C. neoformans/C. gattii species complexes. Whole genome analysis and in vivo virulence studies would clarify the evolution of the genetic diversity and/or virulence of isolates of the C. neoformans/C. gattii species complexes during the pre- and post-HIV-pandemic eras. Since the beginning of the HIV pandemic in 1980, infections due to isolates of the Cryptococcus neoformans/C. gattii species complexes have caused many deaths worldwide, especially in the HIV-infected population. Annually, approximately one-third, of all AIDS-related deaths,—representing more than 1,000,000 cases,—are caused by cryptococcosis. Since 1980, extensive molecular epidemiological surveys have been conducted, and the VNI molecular type has been found to be responsible for more than 90% of cryptococcosis in HIV patients. Whether the high VNI prevalence is associated with the HIV pandemic remains controversial as information on the isolates of the pre-HIV pandemic era is lacking. Therefore, this study of the molecular epidemiology and in vitro characteristics of the strains from the pre-HIV-pandemic era was undertaken. We found that only 64% of cryptococcosis was caused by VNI, and 9 sequence types existed only in the pre-HIV pandemic era. Unlike what was already known about the strains collected during the HIV pandemic era, ST5 and VGIIIa,—supposedly high virulence genotypes,—did not express higher virulence factors than other genotypes. These results implied that the HIV pandemic altered both the molecular epidemiology and virulence of Cryptococcus neoformans/C. gattii species complexes have been altered during HIV pandemic. However, detailed mechanism of these alteration remains to be deciphered further.
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Jiang L, Zhao S, Cai X, Mu D, Zhang X, Kang J, Zhao L, Chen Y. Sequence-based typing of clinical and environmental Legionella pneumophila isolates in Shenyang, China. Enferm Infecc Microbiol Clin 2020; 39:S0213-005X(20)30243-3. [PMID: 32718496 DOI: 10.1016/j.eimc.2020.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/29/2020] [Accepted: 06/04/2020] [Indexed: 11/20/2022]
Abstract
INTRODUCTION We performed SBT (sequence-based typing) on clinical and environmental Legionellapneumophila isolates in Shenyang (China). We analyzed and compared the results with those obtained by PFGE (pulsed field gel electrophoresis). METHODS Twenty-two L. pneumophila isolates were collected from two patients with L. pneumophila infection, two hospitals, and 13 office buildings. There were two clinical isolates, one strain isolated from domestic tap water, another from shower water and 18 strains from cooling tower water. All these isolates were analyzed by SBT and PFGE methods. RESULTS The 22 isolates were divided into 7 types by SBT. Five isolates belonged to novel sequence types (ST2345, ST2344, ST2406, ST2407, and ST2408) and one isolate belonged to ST328. The STs were not obtained for two of the isolates. The remaining 14 isolates belonged to ST1. PFGE typing divided the 22 isolates into 14 pulsotypes. The main pulsotype was SYC, which included seven isolates. CONCLUSION Both typing methods showed that predominant clonal lines exist in the Shenyang region, with high levels of genetic polymorphisms. Five novel STs were identified, indicating a unique genetic composition of L. pneumophila strains in this region, which are significantly different from those found in other environmental water systems in the world.
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Affiliation(s)
- Luxi Jiang
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China; Department of Respiratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Sihong Zhao
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China; Department of Respiratory Medicine, the First Hospital of Shijiazhuang, Hebei, China
| | - Xu Cai
- Institute of Respiratory Disease, The First Hospital of China Medical University, Shenyang, China
| | - Deguang Mu
- Department of Respiratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Xianghua Zhang
- Department of Respiratory Medicine, the First Hospital of Shijiazhuang, Hebei, China
| | - Jian Kang
- Institute of Respiratory Disease, The First Hospital of China Medical University, Shenyang, China
| | - Li Zhao
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yu Chen
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
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Al-Zahrani IA, Al-Ahmadi BM. Dissemination of VIM-producing Pseudomonas aeruginosa associated with high-risk clone ST654 in a tertiary and quaternary hospital in Makkah, Saudi Arabia. J Chemother 2020; 33:12-20. [PMID: 32602782 DOI: 10.1080/1120009x.2020.1785741] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
To the best of our knowledge, no molecular surveillance that has been conducted to identify the most common clones of carbapenem-resistant Pseudomonas aeruginosa (CRPA) in western Saudi Arabia. Therefore, this study aimed to identify genetic diversity and the most common CRPA clones in this region. Thirty-five CRPA isolates were collected from a tertiary and quaternary hospital in Makkah. bla VIM was the most common carbapenemase-encoding gene (11 CRPA isolates), while blaGES was reported in only three isolates. CRPA isolates were subjected to multi- locus sequence typing and showed relatively high genetic diversity with 20 sequence types. Approximately one-third (31.4%) of the CRPA isolates belonged to two high-risk clones (ST235 and ST654). This troublesome finding raises serious concerns about the emergence and further dissemination of CRPA high-risk clones in local hospitals and suggest that surveillance programs should be established in this region to monitor and control clonal dissemination of all multidrug resistant bacteria, including CRPA.
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Affiliation(s)
- Ibrahim A Al-Zahrani
- Faculty of Applied Medical Sciences, Medical Laboratory Technology Department, King Abdulaziz University, Jeddah, Saudi Arabia.,Special infectious Agents Unit-Biosafety Level-3, King Fahad Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Bashaer M Al-Ahmadi
- Faculty of Applied Medical Sciences, Medical Laboratory Technology Department, King Abdulaziz University, Jeddah, Saudi Arabia
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Xu W, Chen T, Wang H, Zeng W, Wu Q, Yu K, Xu Y, Zhang X, Zhou T. Molecular Mechanisms and Epidemiology of Fosfomycin Resistance in Staphylococcus aureus Isolated From Patients at a Teaching Hospital in China. Front Microbiol 2020; 11:1290. [PMID: 32670230 PMCID: PMC7332539 DOI: 10.3389/fmicb.2020.01290] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 05/20/2020] [Indexed: 12/14/2022] Open
Abstract
Staphylococcus aureus is a major cause of hospital- and community-acquired infections placing a significant burden on the healthcare system. With the widespread of multidrug-resistant bacteria and the lack of effective antibacterial drugs, fosfomycin has gradually attracted attention as an "old drug." Thus, investigating the resistance mechanisms and epidemiology of fosfomycin-resistant S. aureus is an urgent requirement. In order to investigate the mechanisms of resistance, 11 fosfomycin-resistant S. aureus isolates were analyzed by PCR and sequencing. The genes, including fosA, fosB, fosC, fosD, fosX, and tet38, as well as mutations in murA, glpT, and uhpT were identified. Quantitative real-time PCR (qRT-PCR) was conducted to evaluate the expression of the target enzyme gene murA and the efflux pump gene tet38 under the selection pressure of fosfomycin. Furthermore, multilocus sequence typing (MLST) identified a novel sequence type (ST 5708) of S. aureus strains. However, none of the resistant strains carried fosA, fosB, fosC, fosD, and fosX genes in the current study, and 12 distinct mutations were detected in the uhpT (3), glpT (4), and murA (5) genes. qRT-PCR revealed an elevated expression of the tet38 gene when exposed to increasing concentration of fosfomycin among 8 fosfomycin-resistant S. aureus strains and reference strain ATCC 29213. MLST analysis categorized the 11 strains into 9 STs. Thus, the mutations in the uhpT, glpT, and murA genes might be the primary mechanisms underlying fosfomycin resistance, and the overexpression of efflux pump gene tet38 may play a major role in the fosfomycin resistance in these isolates.
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Affiliation(s)
- Wenya Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Tao Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Huihui Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Weiliang Zeng
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Qing Wu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Kaihang Yu
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Ye Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiucai Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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May C, Guthrie AJ, Schulman ML. In‐treatment monitoring and use of a novel topical therapy shorten the duration to eliminate
Taylorella asinigenitalis
in donkey stallions. VETERINARY RECORD CASE REPORTS 2020. [DOI: 10.1136/vetreccr-2020-001082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Catherine May
- Department of Production Animal StudiesUniversity of Pretoria Faculty of Veterinary SciencePretoriaSouth Africa
| | - Alan John Guthrie
- Equine Research CentreUniversity of Pretoria Faculty of Veterinary SciencePretoriaSouth Africa
| | - Martin Lance Schulman
- Department of Production Animal StudiesUniversity of Pretoria Faculty of Veterinary SciencePretoriaSouth Africa
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Verma AK, Abdel-Glil MY, Madesh A, Gupta S, Karunakaran AC, Inbaraj S, Abhishek, Nagaleekar VK, Chaudhuri P, Agarwal RK, Thomas P. Multilocus sequence typing of Clostridium perfringens strains from neonatal calves, dairy workers and associated environment in India. Anaerobe 2020; 63:102212. [PMID: 32413405 DOI: 10.1016/j.anaerobe.2020.102212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 04/26/2020] [Accepted: 05/11/2020] [Indexed: 02/08/2023]
Abstract
Clostridium perfringens is a globally recognized zoonotic pathogen. We report isolation and genotyping of C. perfringens from neonatal calves, dairy workers and their associated environment in India. A total of 103 fecal samples from neonatal calves, 25 stool swabs from the dairy workers and 50 samples from their associated environment were collected from two dairy farms. C. perfringens was detected in 26 out of 103 (25.2%) neonatal calf samples, 7 out of 25 (28%) human stool samples and 17 out of 50 (34%) environmental samples. C. perfringens type A strains were predominant in neonatal calves (24/26; 92.3%) and associated environment (15/17; 88.2%). In contrast, strains from dairy workers mostly belonged to type F (5/7; 71.4%), which also carried the beta2 toxin gene. Seventeen strains were analyzed by multilocus sequence typing (MLST) for studying genotypic relationship along with 188 C. perfringens strains available from public databases. A total of 112 sequence types (STs) were identified from 205 C. perfringens strains analyzed. A Clonal complex (CC) represented by three STs (ST 98, ST 41 and ST 110) representing predominantly type F (18/20 strains) were mostly associated with human illnesses. Among predominant STs, ST 54 was associated with enteritis cases in foals and dogs and ST 58 associated with necrotic enteritis in poultry. Seventeen Indian strains were assigned to 13 STs. Genetic relatedness among strains of calves, dairy worker and associated environments indicate inter-host transfers and zoonotic spreads.
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Affiliation(s)
- Asha Kumari Verma
- Division of Veterinary Public Health and Epidemiology, Indian Council for Agricultural Research (ICAR)-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Mostafa Y Abdel-Glil
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96a, 07743, Jena, Germany
| | - Angappan Madesh
- Division of Veterinary Public Health and Epidemiology, Indian Council for Agricultural Research (ICAR)-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Shailendri Gupta
- Division of Bacteriology and Mycology, Indian Council for Agricultural Research (ICAR)- Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Athira Cheruplackal Karunakaran
- Division of Veterinary Public Health and Epidemiology, Indian Council for Agricultural Research (ICAR)-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Sophia Inbaraj
- Division of Bacteriology and Mycology, Indian Council for Agricultural Research (ICAR)- Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Abhishek
- Division of Bacteriology and Mycology, Indian Council for Agricultural Research (ICAR)- Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Viswas Konasagara Nagaleekar
- Division of Bacteriology and Mycology, Indian Council for Agricultural Research (ICAR)- Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Pallab Chaudhuri
- Division of Bacteriology and Mycology, Indian Council for Agricultural Research (ICAR)- Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Rajesh Kumar Agarwal
- Division of Bacteriology and Mycology, Indian Council for Agricultural Research (ICAR)- Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India
| | - Prasad Thomas
- Division of Bacteriology and Mycology, Indian Council for Agricultural Research (ICAR)- Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, Uttar Pradesh, India.
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Gong XQ, Xiao X, Liu JW, Han HJ, Qin XR, Lei SC, Yu XJ. Occurrence and Genotyping of Coxiella burnetii in Hedgehogs in China. Vector Borne Zoonotic Dis 2020; 20:580-585. [PMID: 32301684 DOI: 10.1089/vbz.2019.2589] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Coxiella burnetii is the causative agent of query fever (Q fever), and distributes broadly in environment. Livestock are identified as main reservoirs, which may infect people through their contaminative urine, feces, milk, and birth products. Wild animals can also be the potential carriers and transmitters of C. burnetii. To understand the geographic distribution and host species of C. burnetii in China, we investigated the prevalence of C. burnetii in hedgehogs (Erinaceus amurensis) in Hubei Province. Hedgehogs were tested for C. burnetii with PCR targeting three genes (com1, rrs, and icd) followed by multispacer sequence typing (MST). We found that 12.2% (5/41) hedgehogs were PCR positive for C. burnetii. MST revealed presence of two novel genotypes and phylogenetic analysis revealed that the strains were similar to a group of isolates from chronic Q fever patients and mammals. This study showed that C. burnetii are highly prevalent in hedgehogs in Hubei Province in central China, suggesting that hedgehogs may play an important role in the ecology and transmission of C. burnetii to humans because it is captured and used as traditional medicine in China.
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Affiliation(s)
- Xiao-Qing Gong
- State Key Laboratory of Virology, School of Health Sciences, Wuhan University, Wuhan, China
| | - Xiao Xiao
- State Key Laboratory of Virology, School of Health Sciences, Wuhan University, Wuhan, China.,Lab Animal Research Center, Hubei University of Chinese Medicine, Wuhan, China
| | - Jian-Wei Liu
- State Key Laboratory of Virology, School of Health Sciences, Wuhan University, Wuhan, China
| | - Hui-Ju Han
- State Key Laboratory of Virology, School of Health Sciences, Wuhan University, Wuhan, China
| | - Xiang-Rong Qin
- State Key Laboratory of Virology, School of Health Sciences, Wuhan University, Wuhan, China
| | - Si-Cong Lei
- State Key Laboratory of Virology, School of Health Sciences, Wuhan University, Wuhan, China
| | - Xue-Jie Yu
- State Key Laboratory of Virology, School of Health Sciences, Wuhan University, Wuhan, China
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43
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Verdú-Expósito C, Romanyk J, Cuadros-González J, TesfaMariam A, Copa-Patiño JL, Pérez-Serrano J, Soliveri J. Study of susceptibility to antibiotics and molecular characterization of high virulence Staphylococcus aureus strains isolated from a rural hospital in Ethiopia. PLoS One 2020; 15:e0230031. [PMID: 32163464 PMCID: PMC7067403 DOI: 10.1371/journal.pone.0230031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 02/19/2020] [Indexed: 11/20/2022] Open
Abstract
We characterised 80 Staphylococcus aureus strains isolated from human patients with SSTIs at a rural hospital in Ethiopia. Susceptibility to antibiotic of all strains was tested. The MLST method was used to type and a phylogenetic analysis was conducted employing the sequences of 7 housekeeping genes. PCR amplification was used to investigate the presence of the following virulence genes in all strains: hla (α-haemolysin), tstH (toxic shock syndrome toxin), luk PV (Panton-Valentine leukocidin), fnbA (fibronectin binding protein A) and mecA (methicillin resistance). Most of the strains were resistant to penicillin and ampicillin, but only 3 strains were resistant to oxacillin, and 1 of them was a true MRSA. The MLST results showed a high diversity of sequence types (ST), 55% of which were new, and ST152 was the most prevalent. A phylogeny study showed that many of the new STs were phylogenetically related to other previously described STs, but bore little relationship to the only ST from Ethiopia described in the database. Virulence gene detection showed a high prevalence of strains encoding the hla, fnbA and pvl genes (98.77%, 96.3% and 72.84%, respectively), a low prevalence of the tst gene (13.58%) and a markedly low prevalence of MRSA (1.25%). S. aureus strains isolated from patients in a rural area in Ethiopia showed low levels of antibiotic resistance, except to penicillin. Moreover, this study reveals new STs in Eastern Africa that are phylogenetically related to other previously described STs, and confirm the high prevalence of the pvl gene and the low prevalence of MRSA on the continent.
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Affiliation(s)
- Cristina Verdú-Expósito
- Department of Biomedicine and Biotechnology, University of Alcalá, Alcalá de Henares, Madrid, Spain
| | - Juan Romanyk
- Microbiology Service, Hospital Universitario Príncipe de Asturias, Alcalá-Meco, Alcalá de Henares, Madrid, Spain
| | - Juan Cuadros-González
- Microbiology Service, Hospital Universitario Príncipe de Asturias, Alcalá-Meco, Alcalá de Henares, Madrid, Spain
| | - Abraham TesfaMariam
- Department of General Medicine, Gambo General Rural Hospital, West-Arsi, Ethiopia
| | - José Luis Copa-Patiño
- Department of Biomedicine and Biotechnology, University of Alcalá, Alcalá de Henares, Madrid, Spain
| | - Jorge Pérez-Serrano
- Department of Biomedicine and Biotechnology, University of Alcalá, Alcalá de Henares, Madrid, Spain
| | - Juan Soliveri
- Department of Biomedicine and Biotechnology, University of Alcalá, Alcalá de Henares, Madrid, Spain
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Overview of spatio-temporal distribution inferred by multi-locus sequence typing of Taylorella equigenitalis isolated worldwide from 1977 to 2018 in equidae. Vet Microbiol 2020; 242:108597. [PMID: 32122601 DOI: 10.1016/j.vetmic.2020.108597] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 01/29/2023]
Abstract
The accurate identification of Taylorella equigenitalis strains is essential to improve worldwide prevention and control strategies for contagious equine metritis (CEM). This study compared 367 worldwide equine strains using multilocus sequence typing according to the geographical origin, isolation year and equine breed. The strains were divided into 49 sequence types (STs), including 10 described for the first time. Three major and three minor clonal complexes (CCs), and 11 singletons, were identified. The genetic heterogeneity was low (0.13 STs/strain) despite the wide diversity of geographical origins (n = 16), isolation years (1977-2018) and equine breeds (n = 18). It was highest outside Europe and in the 1977-1997 period; current major STs and CCs already existed before 1998. Previous data associated the major CC1 with the first CEM outbreaks in 1977-1978 in the United Kingdom, Australia and the United States, and revealed its circulation in France. Our study confirms its circulation in France over a longer period of time (1992-2018) and its distribution in Spain and Germany but not throughout Europe. In addition to CC1, relationships between non-European and European countries were observed only through ST4, ST17 and ST30. Within Europe, several STs emerged with cross-border circulation, in particular ST16 and ST46 from the major complexes CC2 and CC8. These results constitute a baseline for monitoring the spread of CEM outbreaks. A retrospective analysis of a higher number of strains isolated worldwide between 1977 and the early 2000s would be helpful to obtain an exhaustive picture of the original CEM situation.
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45
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Ribotyping: a tool for molecular taxonomy. Anim Biotechnol 2020. [DOI: 10.1016/b978-0-12-811710-1.00017-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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46
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Uenoyama K, Ueno Y, Tosaki K, Abeto Y, Ito H, Katsuda K, Shibahara T. Immunohistochemical and molecular analysis of Pasteurella multocida in a rabbit with suppurative pleuropneumonia. J Vet Med Sci 2019; 82:89-93. [PMID: 31801931 PMCID: PMC6983660 DOI: 10.1292/jvms.19-0561] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A 1-month-old rabbit, imported as a pet by a distributor, died suddenly in the quarantine period in Japan due to suppurative pleuropneumonia. A bacterial isolate from its right lung was
identified as Pasteurella multocida serotype A: 11. The isolate was classified as ST204 using the RIRDC scheme of multilocus sequence typing, suggesting that the isolate was
genetically related to European isolates of the same sequence type listed in the PubMLST database and not to four other isolates that originated from past imported rabbits. In the
immunohistochemical assay, an antiserum recognizing the somatic serotype 11 antigen generated from chicken could specifically detect P. multocida, indicating that the
antiserum for somatic serotyping was useful for immunohistochemical diagnosis of rabbit pasteurellosis.
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Affiliation(s)
- Kei Uenoyama
- Pathological and Physiochemical Examination Division, Laboratory Department, Animal Quarantine Service, 11-1 Haramachi, Isogo, Yokohama, Kanagawa 235-0008, Japan
| | - Yuichi Ueno
- Division of Bacterial and Parasitic Disease, National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Kaori Tosaki
- Tochigi Prefectural Kenou Livestock Hygiene Service Center, 6-8 Hiraidekogyodanchi, Utsunomiya, Tochigi 321-0905, Japan
| | - Yusuke Abeto
- Kagoshima Prefectural Kimotsuki Livestock Health and Hygiene Center,145-1 Nishiharaigawatyou, Kanoya, Kagoshima 893-0025, Japan
| | - Hirotaka Ito
- Hiroshima Prefectural Western Livestock Hygiene Service Center, 1-15 Saizyougozyoucho, Higashihiroshima, Hiroshima 739-0013, Japan
| | - Ken Katsuda
- Division of Bacterial and Parasitic Disease, National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan
| | - Tomoyuki Shibahara
- Division of Pathology and Pathophysiology, National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), 3-1-5 Kannondai, Tsukuba, Ibaraki 305-0856, Japan.,Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku-oraikita, Izumisano, Osaka 598-8531, Japan
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Aggarwal S, Jena S, Panda S, Sharma S, Dhawan B, Nath G, Singh NP, Nayak KC, Singh DV. Antibiotic Susceptibility, Virulence Pattern, and Typing of Staphylococcus aureus Strains Isolated From Variety of Infections in India. Front Microbiol 2019; 10:2763. [PMID: 31866962 PMCID: PMC6904308 DOI: 10.3389/fmicb.2019.02763] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/12/2019] [Indexed: 01/10/2023] Open
Abstract
Staphylococcus aureus is one of the major causes of nosocomial infections. This organism produces powerful toxins and cause superficial lesions, systemic infections, and several toxemic syndromes. A total of 109 S. aureus strains isolated from a variety of infections like ocular diseases, wound infection, and sputum were included in the study. Minimum inhibitory concentration (MIC) was determined against 8 antimicrobials. PCR determined the presence of 16S rRNA, nuc, mecA, czrC, qacA/B, pvl, and toxin genes in S. aureus isolates. Pulse-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST), SCCmec, spa-, and agr-typing and serotyping determined the diversity among them. All isolates of S. aureus were resistant to two or more than two antibiotics and generated 32 resistance patterns. These isolates were positive for 16S rRNA and S. aureus-specific nuc gene, but showed variable results for mecA, czrC, and qacA/B and pvl genes. Of the 32 methicillin-resistant S. aureus (MRSA), 13 strains carried SCCmec type V, seven type IV, two type III, and nine carried unreported type UT6. Of the 109 strains, 98.2% were positive for hlg, 94.5% for hla, 86.2% for sei, 73.3% for efb, 70.6% for cna, 30.2% for sea, and 12.8% for sec genes. Serotypes VII and VI were prevalent among S. aureus strains. PFGE analysis grouped the 109 strains into 77 clusters. MLST classified the strains into 33 sequence types (ST) and eight clonal complexes (CCs) of which 12 were singletons, and two belong to new allelic profiles. Isolates showed 46 spa-types that included two new spa-types designated as t14911 and t14912. MRSA and methicillin-susceptible S. aureus (MSSA) isolates were diverse in terms of antibiotic resistance pattern, toxin genotypes, SCCmec types, serotypes and PFGE, MLST, and spa-types. However, few isolates from eye infection and wound infection belong to CC239, ST239, and spa-type t037/t657. The study thus suggests that S. aureus strains are multidrug resistant, virulent, and diverse irrespective of sources and place of isolation. These findings necessitate the continuous surveillance of multidrug-resistant and virulent S. aureus and monitoring of the transmission of infection.
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Affiliation(s)
- Shifu Aggarwal
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Smrutiti Jena
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Sasmita Panda
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Savitri Sharma
- Jhaveri Microbiology Centre, LV Prasad Eye Institute, Brien Holden Eye Research Centre, Kallam Anji Reddy Campus, Hyderabad, India
| | - Benu Dhawan
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Gopal Nath
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - N P Singh
- Department of Microbiology, Faculty of Medical Sciences, University of Delhi, New Delhi, India
| | | | - Durg Vijai Singh
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, India.,Department of Biotechnology, Central University of South Bihar, Gaya, India
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Vaiyapuri M, Joseph TC, Rao BM, Lalitha KV, Prasad MM. Methicillin-Resistant Staphylococcus aureus in Seafood: Prevalence, Laboratory Detection, Clonal Nature, and Control in Seafood Chain. J Food Sci 2019; 84:3341-3351. [PMID: 31769517 DOI: 10.1111/1750-3841.14915] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/04/2019] [Accepted: 10/08/2019] [Indexed: 11/30/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA), a versatile pathogen bearing multiple virulence determinants, is increasingly being detected in various food-producing animals, including fish. In addition, it is a potential food poisoning agent. MRSA is not an inherent microbiota of fish; its presence is attributed to pre- or postharvest contamination through fish handlers, water, ice, and processing equipment. Several reviews have been written on MRSA in clinical as well as the food animal-producing sector, but information specific to MRSA in seafood is scant. This review puts forth insights on MRSA detection in seafood, antibiotic resistance, diversity of clones in seafood, and possible control measures in seafood production chain. Emphasis has been given on assessing the variations in the protocols employed for isolation and identification in different food matrices and lay the foundation for researchers to develop optimized procedure.
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Affiliation(s)
- Murugadas Vaiyapuri
- Microbiology, Fermentation and Biotechnology (MFB) Division, ICAR-Central Inst. of Fisheries Technology (ICAR-CIFT), Willingdon Island, Cochin, 682029, India
| | | | | | | | - Mothadaka Mukteswar Prasad
- Microbiology, Fermentation and Biotechnology (MFB) Division, ICAR-Central Inst. of Fisheries Technology (ICAR-CIFT), Willingdon Island, Cochin, 682029, India
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Matsumoto Y, Kinjo T, Motooka D, Nabeya D, Jung N, Uechi K, Horii T, Iida T, Fujita J, Nakamura S. Comprehensive subspecies identification of 175 nontuberculous mycobacteria species based on 7547 genomic profiles. Emerg Microbes Infect 2019; 8:1043-1053. [PMID: 31287781 PMCID: PMC6691804 DOI: 10.1080/22221751.2019.1637702] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The prevalence of nontuberculous mycobacteria (NTM) pulmonary diseases has been increasing worldwide. NTM consist of approximately 200 species and distinguishing between them at the subspecies level is critical to treatment. In this study, we sequenced 63 NTM genomes, 27 of which were newly determined, by hybrid assembly using sequencers from Illumina and Oxford Nanopore Technologies (ONT). This analysis expanded the available genomic data to 175 NTM species and redefined their subgenus classification. We also developed a novel multi-locus sequence typing (MLST) database based on 184 genes from 7547 assemblies and an identification software, mlstverse, which can also be used for detecting other bacteria given a suitable MLST database. This method showed the highest sensitivity and specificity amongst conventional methods and demonstrated the capacity for rapid detection of NTM, 10 min of sequencing of the ONT MinION being sufficient. Application of this methodology could improve disease epidemiology and increase the cure rates of NTM diseases.
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Affiliation(s)
- Yuki Matsumoto
- a Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases , Osaka University , Suita , Japan
| | - Takeshi Kinjo
- b Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine , University of the Ryukyus , Nakagami-gun , Japan
| | - Daisuke Motooka
- a Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases , Osaka University , Suita , Japan.,c Laboratory of Pathogen Detection and Identification, International Research Center for Infectious Diseases, Research Institute for Microbial Diseases , Osaka University , Suita , Japan
| | - Daijiro Nabeya
- b Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine , University of the Ryukyus , Nakagami-gun , Japan
| | - Nicolas Jung
- a Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases , Osaka University , Suita , Japan
| | - Kohei Uechi
- b Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine , University of the Ryukyus , Nakagami-gun , Japan.,d Division of Clinical Laboratory and Blood Transfusion , University of the Ryukyus Hospital , Nakagami-gun , Japan
| | - Toshihiro Horii
- a Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases , Osaka University , Suita , Japan
| | - Tetsuya Iida
- a Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases , Osaka University , Suita , Japan
| | - Jiro Fujita
- b Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine , University of the Ryukyus , Nakagami-gun , Japan
| | - Shota Nakamura
- a Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases , Osaka University , Suita , Japan.,c Laboratory of Pathogen Detection and Identification, International Research Center for Infectious Diseases, Research Institute for Microbial Diseases , Osaka University , Suita , Japan.,e Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives , Osaka University , Suita , Japan
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50
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Campylobacter heat resistance - past, current status and future prospect for New Zealand and beyond. WORLD POULTRY SCI J 2019. [DOI: 10.1017/s0043933915000100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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